Re: [Freesurfer] Resolution limits of FLAIR/T2w for effective pial refinement

[Glasser, Matthew]

The trouble with highly anisotropic resolutions is that your resolution is
only as good as your worst axis for the convoluted cerebral cortex.  0.8mm
or better would be optimal given a minimum cortical thickness of 1.6mm.

You can always try with what you have and see if it is net beneficial or
not.  

Peace,

Matt.

On 2/28/18, 12:40 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Christopher Markiewicz"  wrote:

>Hi all,
>
>I wonder if people have any data (or anecdotes - I'm not picky) with
>regard to how high of resolution T2w or FLAIR images need to be in order
>to be useful for FreeSurfer's pial refinement. I've seen a couple threads
>suggesting the optimal is ~1mm isotropic, and that thick slice (1x1x5
>mm^3) FLAIR images could be tried, but might hurt more than help, and I'm
>wondering if there's a suboptimal-but-still-useful range somewhere in
>between.
>
>For the record, this isn't a question of what scan parameters are
>recommended, but rather is in the context of data that's already been
>collected, which I would like to preprocess as well as possible.
>
>So, at what resolutions would you recommend (a) completely ignoring
>T2w/FLAIR images; (b) including T2w/FLAIR images that pass QC; (c) trying
>and seeing? Do these answers change at all with T1w resolution?
>
>--
>Chris Markiewicz
>Center for Reproducible Neuroscience
>Stanford University
>
>
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Re: [Freesurfer] Collecting 2 T1s Best?

[Glasser, Matthew]

Are you getting a 0.8mm isotropic T2w or FLAIR?  You would probably get better 
mileage out of a different type of scan that can help exclude dura and blood 
vessels if you aren’t already getting one.  Also what coil are you using?  I 
might prefer a TI=1000ms simply because it spreads the CSF, GM, and WM 
histogram peaks out a little more evenly, whereas 1060 will have GM and WM 
closer together than GM and CSF.

Peace,

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Alessandra Macbeth 
mailto:alessandramacb...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, March 7, 2018 at 1:29 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Collecting 2 T1s Best?

Hi there,

I know in the past, it was recommended to acquire 2 T1 scans so that they could 
be averaged for better SNR, etc. in order to improve cortical thickness and 
surface area measurements. Is this still the recommendation? We have a few 
extra minutes in our scanning protocol and are debating whether to include a 
2nd T1.

Our parameters are: MPRAGE with .8mm^3 voxel size, slice thickness of .8, FA = 
8 degrees, TR = 2400ms, TE = 2.72ms, TI = 1060ms.

Best,
Alessandra

--
Alessandra Macbeth, M.A.
Doctoral Candidate - Department of Psychology
University of California, Riverside
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Re: [Freesurfer] inherent smoothing

[Glasser, Matthew]

External Email - Use Caution

You can do this in Connectome Workbench with wb_command
-metric-estimate-fwhm if you convert the thickness map and surface to
GIFTI with mris_convert.

Peace,

Matt.

On 5/9/18, 2:14 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N. Greve"  wrote:

>Not that I know of. I don''t know what it would mean
>
>
>
>On 05/09/2018 12:14 PM, Joost Janssen wrote:
>>
>>
>> Can it be done without (before) running a group analysis?
>> Thanks,
>> -joost
>> 
>>>4486> 
>>
>>
>>
>>
>> On Tue, May 8, 2018 at 6:07 PM, Douglas N. Greve
>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>
>> If you run a group analysis, there will be a fwhm.dat file with the
>> estimate of the Gaussian full width half max. The smoothess is not
>> Gaussian, but it gives a measure. Does that work?
>>
>>
>> On 05/08/2018 04:20 AM, Joost Janssen wrote:
>> >
>> >
>> > Dear Doug,
>> >
>> > I'd like to determine the inherent smoothing of ?h.thickness in my
>> > sample. What is the best way to do this?
>> >
>> > Thanks,
>> > -joost
>> >
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> 
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>>
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>>
>> The information in this e-mail is intended only for the person to
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>> contains patient information, please contact the Partners
>> Compliance HelpLine at
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Re: [Freesurfer] missing ribbon.mgz

[Glasser, Matthew]

External Email - Use Caution

Did you run the preceding steps of FreeSurfer?  Does that file exist?

Peace,

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Aaron Tanenbaum 
mailto:aaron.b.tanenb...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:Freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, July 13, 2018 at 5:24 PM
To: Freesurfer 
mailto:Freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] missing ribbon.mgz


External Email - Use Caution

I am a bit puzzled. I am running freesurfer 5.3 HCP on ubuntu 14.04.  I am 
getting an error, see below
I am using the command

recon-all -s BOLD-52_v1 -mprage -autorecon2
This has happened before. What did I do wrong.



#@# ASeg Stats Fri Jul 13 12:55:02 CDT 2018

INFO: mri_segstats will not calculate Supratentorial
  due to missing ribbon.mgz file
/data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1

 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz 
--empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 
--excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm 
--in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler 
--ctab /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject 
BOLD-52_v1


$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg 
--excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab 
/data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject BOLD-52_v1
sysname  Linux
hostname brahms
machine  x86_64
user tanenbauma
UseRobust  0
atlas_icv (eTIV) = 1714974 mm^3(det: 1.135939 )
mghRead(/data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1/mri/ribbon.mgz, 
-1): could not open file
Computing euler number
orig.nofix lheno =  -70, rheno = -38
orig.nofix lhholes =   36, rhholes = 20
Loading mri/aseg.mgz
Getting Brain Volume Statistics
Linux brahms 3.19.0-80-generic #88~14.04.1-Ubuntu SMP Fri Jan 13 14:54:07 UTC 
2017 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s BOLD-52_v1 exited with ERRORS at Fri Jul 13 12:55:11 CDT 2018

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting





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Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics between groups analyses

[Glasser, Matthew]

External Email - Use Caution

If you have only two protocols “high quality” and “low quality", you could 
presumably include a protocol variable as a covariate of no interest, thereby 
removing any effects that correlate with protocol.  For this to work ideally, 
you would have similar numbers of low and high quality protocols across your 
comparison groups.  I agree with Doug that SNR will generally tend to make 
results more variable, but not necessarily in a specific direction.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas Greve 
mailto:dgr...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, August 5, 2018 at 4:48 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics 
between groups analyses

I thought I answered this question last week. See my rsponse below

I don't think it is correct conceptually.  By including SNR as a covariate, you 
are saying that you expect the thickness to increase with higher SNR and 
decrease with lower SNR. This does not make sense to me. It sounds like you are 
trying to do a mixed effects analysis where you weight by the SNR. Still, 
mathematically, this is not a true mixed effect analysis (which requires 
estimates of the within and between subject noise). `

On 8/3/18 10:57 AM, John Anderson wrote:

External Email - Use Caution

Daer FS experts,
I would like to inquire about including SNR as a covariate for the between 
groups cpmparison in cortical thickness. Is this procedure correct 
mathematically? Do I need to demean the SNA values before including it 
covariates? Finally, do you recommend any quality parameters other than SNR to 
be included covariate?

I look forward to learn from your expertise,
Thanks,
John


On 8/5/18 1:04 PM, John Anderson wrote:

External Email - Use Caution

Dear FS experts,
I would like to inquire about including SNR as a covariate for the between 
groups comparison in cortical thickness. Is this procedure valid? I have some 
T1 images of low quality and the majority are high in quality. I reviewed the 
segmentation and the cortical surfaces and fixed manually as possible. I don't 
want to exclude images from the data sets, so I am thinking of regressing out 
SNR.
It seems that the command "mri_segstats" can report SNR for every ROI in the 
brain. Is it correct to include whole brain SNR covariate for between group 
comparisons (cortical thickness and volumetric analyses).
If yes, do I need to include actual SNR values in the FSGD file or the demeaned 
values ?

We appreciate your guidance!
John




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Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

[Glasser, Matthew]

External Email - Use Caution

How about running FreeSurfer on your T1w image?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Renew Andrade 
mailto:andradere...@yahoo.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, August 5, 2018 at 9:13 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] ERROR: input(s) cannot have multiple frames!


External Email - Use Caution

Hello community!

I have an issue while running recon-all -all in a dpi file. What do you suggest 
as a solution?
Thank you!

Renes-MacBook-Air-2:~ andraderenew$ recon-all -all  -i 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz
   -s Parkinson_p06316_dwi_2500
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir
Actual FREESURFER_HOME /Applications/freesurfer
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500
\n mri_convert 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz
 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
 \n
mri_convert.bin 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz
 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0.973179, 0.23005)
k_ras = (0, -0.23005, 0.973179)
writing to 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz...
#
#@# MotionCor Sun Aug  5 21:11:50 -05 2018
Found 1 runs
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
 has 121 frames
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64

recon-all -s Parkinson_p06316_dwi_2500 exited with ERRORS at Sun Aug  5 
21:11:50 -05 2018

For more details, see the log file 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] WM segmentation

[Glasser, Matthew]

External Email - Use Caution

Perhaps erosion was suggested because of partial voluming in your fMRI voxels.

Peace,

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Ben M mailto:fmri@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, August 6, 2018 at 9:27 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] WM segmentation


External Email - Use Caution

Hi,
I would like to create a mask of the WM for fMRI analysis. I read a previous 
post in which it was suggested to get the wm segmentation and erode it, since 
the result will be exclusively WM. My question is why is this so? Why can I 
assume that getting the WM mask from the aseg file will almost certainly get me 
high probability WM, >0.9 for example? In most segmentation algorithms we get 
posterior probabilities at each voxel, so that we can then select voxels with 
posterior probabilities >0.90 for example. Why is freesurfer's WM segmentation 
so accurate that we do not need posterior probabilities? Are these very high 
probabilities somehow already coded in freesurfer's segmentation algorithm?
Thanks,
Ben


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Re: [Freesurfer] WM segmentation

[Glasser, Matthew]

External Email - Use Caution

I would add that a properly eroded WM mask is not very effective for fMRI
denoising at least relative to spatial and temporal ICA-based denoising.
An uneroded mask behaves similarly to global signal regression, which
removes both global noise and global neural signal.

Matt.

On 8/7/18, 4:22 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

>1. You can dig up our old 1999 recon papers if you are really interested.
>Lots of segmentation techniques are not probabilistic.
>
>2. Again, we don't output probabilities. YOu are better off eroding as
>Matt
>suggested.
>
>3. mris_fill fills the interior of a surface - nothing to do with
>mri_fill.
>
>If all you want is a nuisance regressor just take the wm.mgz, or interior
>of the white surface and erode it once, then use those voxels
>Bruce
>
>
>On Tue, 7 Aug 2018, Ben M wrote:
>
>>
>> External Email - Use Caution
>>
>> Hi Bruce,
>>
>> Thank you very much for your reply. The idea is to create a WM mask
>>that I can use for the denoising
>> step of resting state connectivity analysis. Do you mind if I ask you a
>>few follow up questions?
>>
>> 1 - "our primary cortical segmentation of the wm is not probabilistic."
>> How is the segmentation of the WM achieved in freesurfer then, if not
>>probabilistic?
>>
>> 2 - "In any case you want partial volume fractions I expect, not
>>posterior probabilities."
>> Sorry, I'm not sure what you mean by partial volume fractions. In
>>several papers I have read the WM
>> is first thresholded (eg p >.9) to ensure that only WM voxels are
>>included in the mask, which is
>> also eroded. Are the values being thresholded partial volume fractions
>>then, and not probabilities?
>> But if segmentation is done on tissue probability maps (eg like in SPM
>>I think), wouldn't you have
>> probabilities? Or do you mean you have partial volume fractions just in
>>freesurfer?
>>
>> 3 - "I would use mris_fill to create a mask of the WM from the ?h.white
>>surfaces, if you want the
>> most accuracy"
>> I found more information about the command mri_fill than mris_fill, is
>>there a difference between
>> the two, or can I use both for the same thing?
>>
>> Sorry for the newbie questions, I am just beginning using freesurfer.
>>
>> Best
>> Ben
>>
>> On Tue, Aug 7, 2018 at 6:08 PM, Bruce Fischl
>> wrote:
>>   Hi Ben
>>
>>   our primary cortical segmentation of the wm is not probabilistic.
>>In any case you want
>>   partial volume fractions I expect, not posterior probabilities. I
>>would use mris_fill to
>>   create a mask of the WM from the ?h.white surfaces, if you want
>>the most accuracy
>>
>>   cheers
>>   Bruce
>>
>>   On Tue, 7 Aug 2018, Ben M wrote:
>>
>>
>> External Email - Use Caution
>>
>> Hi,
>> I would like to create a mask of the WM for fMRI analysis.
>>I read a previous
>> post in which it was
>> suggested to get the wm segmentation and erode it, since
>>the result will be
>> exclusively WM. My
>> question is why is this so? Why can I assume that getting
>>the WM mask from
>> the aseg file will almost
>> certainly get me high probability WM, >0.9 for example? In
>>most segmentation
>> algorithms we get
>> posterior probabilities at each voxel, so that we can then
>>select voxels
>> with posterior
>> probabilities >0.90 for example. Why is freesurfer's WM
>>segmentation so
>> accurate that we do not need
>> posterior probabilities? Are these very high probabilities
>>somehow already
>> coded in freesurfer's
>> segmentation algorithm?
>> Thanks,
>> Ben
>>
>>
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>> The information in this e-mail is intended only for the person to whom
>>it is
>> addressed. If you believe this e-mail was sent to you in error and the
>>e-mail
>> contains patient information, please contact the Partners Compliance
>>HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in error
>> but does not contain patient information, please contact the sender and
>>properly
>> dispose of the e-mail.
>>
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Re: [Freesurfer] Parcellations (e.g., labels for Brodmann Areas) for Connectome Workbench?

[Glasser, Matthew]

External Email - Use Caution

FYI: Connectome Workbench is comparable with NIFTI/GIFTI/CIFTI formats.  GIFTI 
includes .surf.gii, .label.gii, .shape.gii, .func.gii.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Dinicola, Lauren" 
mailto:lmd...@g.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, September 7, 2018 at 3:40 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Parcellations (e.g., labels for Brodmann Areas) for 
Connectome Workbench?

Hi Doug,

I actually got this to work by just changing .aparc.gii to .label.gii & opening 
using the workbench; please disregard, and I apologize for taking your time.

All the best,

Lauren

On Thu, Sep 6, 2018 at 2:47 PM, Dinicola, Lauren 
mailto:lmd...@g.harvard.edu>> wrote:
Hi Doug,

I have successfully converted an individual BA label to a .label.gii file and 
opened it; I have not been able to open the Gifti .aparc.annot file after 
attempting to convert the .annot file in Connectome Workbench. So I am 
wondering if a full parcellation already exists in dlabel.gii format.

Thank you again,

Lauren

On Thu, Sep 6, 2018 at 12:32 PM, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:
what is the compatible format?

On 09/06/2018 11:54 AM, Dinicola, Lauren wrote:
> Hi all,
>
> I have been searching for the Freesurfer label or annot files for
> fsaverage in the formats compatible with Connectome Workbench and have
> not yet found them. Are these available?
> If not, is there a way to convert all the BA labels to then convert
> them to borders for viewing on fsaverage? I tried mris_convert -annot
> but was unsuccessful opening the output files.
>
> Thank you very much for any help.
>
> Lauren
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] denoising and recon-all

[Glasser, Matthew]

External Email - Use Caution

What are you using for denoising?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Lisa Crystal Krishnamurthy 
mailto:lkrishnamur...@gsu.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, October 11, 2018 at 11:05 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] denoising and recon-all


External Email - Use Caution
Hi,

I have found that denoising the MPRAGE prior to FS recon-all seems to improve 
the segmentation (see attached pdf). However, it is not clear if the denoising 
algorithm may cause some signal intensity changes (especially in voxels with 
partial voluming at the edge of the brain) that violate assumptions of 
recon-all. Could you help me understand what the assumptions of your algorithm 
are, and what I need to do to make sure my images conform to those assumptions?

Your help is greatly appreciated.
Best,
-Lisa


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Re: [Freesurfer] acquisition protocols 3T Prisma

[Glasser, Matthew]

External Email - Use Caution

I would particularly recommend the third name on that list, as Mike has done a 
lot of work on the HCP-Style acquisition protocols.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Aaron Tanenbaum 
mailto:aaron.b.tanenb...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, October 19, 2018 at 3:23 PM
To: Freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] acquisition protocols 3T Prisma


External Email - Use Caution

I suggest you talk to the folks at Washington university in St Louis. There has 
been considerable amount of work looking at this.  You should contact the 
following individuals
Steve Petersen  s...@wustl.edu
Avi Snyder   azsny...@wustl.edu
Michael harms mha...@wustl.edu


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Re: [Freesurfer] Myelinated cortical thickness ratio map

[Glasser, Matthew]

External Email - Use Caution

Regression would be better than division.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Damien MARIE mailto:damien.ma...@unige.ch>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, October 22, 2018 at 8:54 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Myelinated cortical thickness ratio map


External Email - Use Caution

Dear experts,

I am working with R1 maps that I project on the surface. The goal is to look at 
intra-cortical myelin.

I detect interesting effects between two groups. Now I would like to compute 
myelinated cortical thickness ratio maps, in order to control for the effect of 
cortical thickness variations occurring with gyrification.

Here is a paper where they describe a way to compute those myelinated cortical 
thickness ratio map with MIPAV and the MPI-CBS toolbox : 
https://www.ncbi.nlm.nih.gov/pubmed/29321232
«  The proportional thickness of the myelinated part of the cortex in relation 
to its overall thickness (myelinated cortical thickness) was computed with a 
fuzzy classification technique combining information about radial and 
tangential fibers.  «

1- Is it possible to do the same in FreeSurfer?

2- What about dividing my individual myelin maps by the individual cortical 
thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do 
the job in the volume but I don’t know how I could do that in FreeSurfer.

Any comments / other suggestions are welcome.

Thank you and best,

Damien




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Re: [Freesurfer] cluster failing on HCP freesurfer script

[Glasser, Matthew]

External Email - Use Caution

What version of FreeSurfer are you using?  Is the FreeSurfer environment set up 
correctly?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Sanchez, Juan (NYSPI)" 
mailto:juan.sanc...@nyspi.columbia.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, October 26, 2018 at 3:12 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] cluster failing on HCP freesurfer script


External Email - Use Caution

Dear community,

My group is using the latest version of condor clustering to process our data 
on OS X.

We have a bash script that calls freesurfer to run our HCP pipelines. I can run 
the script to completion when running it locally on each of the clustered 
machines, however when submitting the job I get the following error

Can’t locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup 
module) (@INC contains: 
/Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 
/Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 
/Network/Library/Perl/5.18/darwin-thread-multi-2level 
/Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 
/System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 
/System/Library/Perl/Extras/5.18/darwin-thread-multi-2level 
/System/Library/Perl/Extras/5.18 .) at 
/Applications/freesurfer/mni/bin/nu_correct line 37.
BEGIN failed--compilation aborted at 
/Applications/freesurfer/mni/bin/nu_correct line 37.
(standard_in) 2: comparison in expression

 Can anyone suggest a solution?
Thanks
J



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Re: [Freesurfer] cluster failing on HCP freesurfer script

[Glasser, Matthew]

External Email - Use Caution

That seems like an old version to me.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Sanchez, Juan (NYSPI)" 
mailto:juan.sanc...@nyspi.columbia.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, October 26, 2018 at 3:43 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] cluster failing on HCP freesurfer script


External Email - Use Caution

Thanks for the reply Matt


freesurfer-i386-apple-darwin11.4.2-stable5-20130514


The scripts run fine outside of condor. So it must be how condor is selecting 
the freesurfer

The Environment is set up correclty




From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Friday, October 26, 2018 4:26:13 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] cluster failing on HCP freesurfer script


ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


External Email - Use Caution

What version of FreeSurfer are you using?  Is the FreeSurfer environment set up 
correctly?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Sanchez, Juan (NYSPI)" 
mailto:juan.sanc...@nyspi.columbia.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, October 26, 2018 at 3:12 PM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] cluster failing on HCP freesurfer script


External Email - Use Caution

Dear community,

My group is using the latest version of condor clustering to process our data 
on OS X.

We have a bash script that calls freesurfer to run our HCP pipelines. I can run 
the script to completion when running it locally on each of the clustered 
machines, however when submitting the job I get the following error

Can’t locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup 
module) (@INC contains: 
/Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 
/Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 
/Network/Library/Perl/5.18/darwin-thread-multi-2level 
/Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 
/System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 
/System/Library/Perl/Extras/5.18/darwin-thread-multi-2level 
/System/Library/Perl/Extras/5.18 .) at 
/Applications/freesurfer/mni/bin/nu_correct line 37.
BEGIN failed--compilation aborted at 
/Applications/freesurfer/mni/bin/nu_correct line 37.
(standard_in) 2: comparison in expression

 Can anyone suggest a solution?
Thanks
J






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intended recipient, be advised that any unauthorized use, disclosure, copying 
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strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
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Re: [Freesurfer] myelination and freesurfer segmentation...

[Glasser, Matthew]

External Email - Use Caution

Hi Bruce,

Perhaps he wants to know about whether changes in myelination will affect
things like estimates of cortical thickness?

Matt.

On 11/2/18, 10:11 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

>Hi Gonzalo
>
>I don't really understand what you are asking. Can you give us more
>details?
>
>cheers
>Bruce
>On Fri, 2 Nov 2018, Gonzalo Rojas Costa wrote:
>
>>External Email - Use Caution
>>
>> Hi:
>>
>>  Could you please tell me if Is there is a paper on myelination and
>> segmentation?
>>
>>  Sincerely,
>>
>>
>> Gonzalo Rojas Costa
>>
>> Laboratory for Advanced Medical Image Processing
>> Department of Radiology
>> Clínica las Condes
>> Lo Fontecilla 441, Las Condes, Santiago, Chile.
>> Tel: 56-2-2105170
>> Cel: 56-9-97771785
>> www.clc.cl
>> http://www.aribrain.info
>> https://scholar.google.com/citations?user=LO7LZ3oJ
>> https://www.researchgate.net/profile/Gonzalo_Rojas2
>> https://cl.linkedin.com/in/gonzalorojascosta
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>



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Re: [Freesurfer] mpr2mni305 failed, during recon-all

[Glasser, Matthew]

External Email - Use Caution

Which version of FreeSurfer is this and did you do some OS upgrade in between?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, December 23, 2018 at 8:24 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] mpr2mni305 failed, during recon-all


External Email - Use Caution

hello,
I'm running the hcp's FreeSurfer pipeline, and for some reason, after working 
successfully several times, on different subjects, im getting this error:
***
/Users/georgieboy/Research/Piano/test/222/222/mri
\n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz \n
\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
Darwin medical613-6.tau.ac.il 18.2.0 Darwin 
Kernel Version 18.2.0: Fri Oct  5 19:41:49 PDT 2018; 
root:xnu-4903.221.2~2/RELEASE_X86_64 x86_64

recon-all -s 222 exited with ERRORS at Sun Dec 23 15:50:23 IST 2018
***

the information in the talairach_avi.log is as follows:

***
dyld: Symbol not found: ___keymgr_global
  Referenced from: /Applications/freesurfer/bin/gauss_4dfp
  Expected in: /usr/lib/libSystem.B.dylib
 in /Applications/freesurfer/bin/gauss_4dfp
Abort
ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134
ERROR: mpr2mni305 execution aborted
***

to be clear, this -  /usr/lib/libSystem.B.dylib exists exactly where is was 
expected...

the input image, orig.mgz, looks fine and is in 1 mm res...
so im having trouble getting to the bottom of the error.

thanks in advance,
Shachar


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Re: [Freesurfer] mpr2mni305 failed, during recon-all

[Glasser, Matthew]

External Email - Use Caution

Is that FreeSurfer 5.3?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, December 23, 2018 at 8:35 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mpr2mni305 failed, during recon-all


External Email - Use Caution

this is my Freesurfer version - 
freesurfer-i386-apple-darwin10.8.0-stable5-20130513

and I think the update to macOS Mojave was after successfully running the 
pipeline.
you think this could be the issue? should I just upgrade my freesurfer?

thanks

On Sun, 23 Dec 2018 at 16:28, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

External Email - Use Caution

Which version of FreeSurfer is this and did you do some OS upgrade in between?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, December 23, 2018 at 8:24 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] mpr2mni305 failed, during recon-all


External Email - Use Caution

hello,
I'm running the hcp's FreeSurfer pipeline, and for some reason, after working 
successfully several times, on different subjects, im getting this error:
***
/Users/georgieboy/Research/Piano/test/222/222/mri
\n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz \n
\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
Darwin medical613-6.tau.ac.il<http://medical613-6.tau.ac.il/> 18.2.0 Darwin 
Kernel Version 18.2.0: Fri Oct  5 19:41:49 PDT 2018; 
root:xnu-4903.221.2~2/RELEASE_X86_64 x86_64

recon-all -s 222 exited with ERRORS at Sun Dec 23 15:50:23 IST 2018
***

the information in the talairach_avi.log is as follows:

***
dyld: Symbol not found: ___keymgr_global
  Referenced from: /Applications/freesurfer/bin/gauss_4dfp
  Expected in: /usr/lib/libSystem.B.dylib
 in /Applications/freesurfer/bin/gauss_4dfp
Abort
ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134
ERROR: mpr2mni305 execution aborted
***

to be clear, this -  /usr/lib/libSystem.B.dylib exists exactly where is was 
expected...

the input image, orig.mgz, looks fine and is in 1 mm res...
so im having trouble getting to the bottom of the error.

thanks in advance,
Shachar


The materials in this message are private and may contain Protected Healthcare 
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Re: [Freesurfer] mpr2mni305 failed, during recon-all

[Glasser, Matthew]

External Email - Use Caution

We’re working on a FS 6.0+ compatible version of the HCP pipelines and 
FreeSurfer that is almost ready.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, December 24, 2018 at 3:12 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Ido Tavor mailto:idota...@gmail.com>>, Niv Tik 
mailto:niv...@gmail.com>>
Subject: Re: [Freesurfer] mpr2mni305 failed, during recon-all


External Email - Use Caution

yes, it is version 5.3.0-HCP
fsbuilds answered that I should upgrade to version 6, but im afraid that it 
lacks the changes you made so the version will suit the HCP Pipelines...

what do you suggest?

thanks,
Shachar

On Sun, 23 Dec 2018 at 17:00, Shachar Gal 
mailto:gal.shac...@gmail.com>> wrote:
Sorry, out of the office for the day. I'll get back to you about it tomorrow

Shachar

On Sun, Dec 23, 2018, 16:56 Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

External Email - Use Caution

Is that FreeSurfer 5.3?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, December 23, 2018 at 8:35 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mpr2mni305 failed, during recon-all


External Email - Use Caution

this is my Freesurfer version - 
freesurfer-i386-apple-darwin10.8.0-stable5-20130513

and I think the update to macOS Mojave was after successfully running the 
pipeline.
you think this could be the issue? should I just upgrade my freesurfer?

thanks

On Sun, 23 Dec 2018 at 16:28, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

External Email - Use Caution

Which version of FreeSurfer is this and did you do some OS upgrade in between?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, December 23, 2018 at 8:24 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] mpr2mni305 failed, during recon-all


External Email - Use Caution

hello,
I'm running the hcp's FreeSurfer pipeline, and for some reason, after working 
successfully several times, on different subjects, im getting this error:
***
/Users/georgieboy/Research/Piano/test/222/222/mri
\n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz \n
\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
Darwin medical613-6.tau.ac.il<http://medical613-6.tau.ac.il/> 18.2.0 Darwin 
Kernel Version 18.2.0: Fri Oct  5 19:41:49 PDT 2018; 
root:xnu-4903.221.2~2/RELEASE_X86_64 x86_64

recon-all -s 222 exited with ERRORS at Sun Dec 23 15:50:23 IST 2018
***

the information in the talairach_avi.log is as follows:

***
dyld: Symbol not found: ___keymgr_global
  Referenced from: /Applications/freesurfer/bin/gauss_4dfp
  Expected in: /usr/lib/libSystem.B.dylib
 in /Applications/freesurfer/bin/gauss_4dfp
Abort
ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134
ERROR: mpr2mni305 execution aborted
***

to be clear, this -  /usr/lib/libSystem.B.dylib exists exactly where is was 
expected...

the input image, orig.mgz, looks fine and is in 1 mm res...
so im having trouble getting to the bottom of the error.

thanks in advance,
Shachar


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received 

Re: [Freesurfer] mpr2mni305 failed, during recon-all

[Glasser, Matthew]

External Email - Use Caution

After the holidays.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, December 24, 2018 at 8:14 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mpr2mni305 failed, during recon-all


External Email - Use Caution

good to hear. looking forward to it. any estimation as to when it will be ready?

Shachar

On Mon, 24 Dec 2018 at 14:25, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

External Email - Use Caution

We’re working on a FS 6.0+ compatible version of the HCP pipelines and 
FreeSurfer that is almost ready.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, December 24, 2018 at 3:12 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Ido Tavor mailto:idota...@gmail.com>>, Niv Tik 
mailto:niv...@gmail.com>>
Subject: Re: [Freesurfer] mpr2mni305 failed, during recon-all


External Email - Use Caution

yes, it is version 5.3.0-HCP
fsbuilds answered that I should upgrade to version 6, but im afraid that it 
lacks the changes you made so the version will suit the HCP Pipelines...

what do you suggest?

thanks,
Shachar

On Sun, 23 Dec 2018 at 17:00, Shachar Gal 
mailto:gal.shac...@gmail.com>> wrote:
Sorry, out of the office for the day. I'll get back to you about it tomorrow

Shachar

On Sun, Dec 23, 2018, 16:56 Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

External Email - Use Caution

Is that FreeSurfer 5.3?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, December 23, 2018 at 8:35 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mpr2mni305 failed, during recon-all


External Email - Use Caution

this is my Freesurfer version - 
freesurfer-i386-apple-darwin10.8.0-stable5-20130513

and I think the update to macOS Mojave was after successfully running the 
pipeline.
you think this could be the issue? should I just upgrade my freesurfer?

thanks

On Sun, 23 Dec 2018 at 16:28, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

External Email - Use Caution

Which version of FreeSurfer is this and did you do some OS upgrade in between?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, December 23, 2018 at 8:24 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] mpr2mni305 failed, during recon-all


External Email - Use Caution

hello,
I'm running the hcp's FreeSurfer pipeline, and for some reason, after working 
successfully several times, on different subjects, im getting this error:
***
/Users/georgieboy/Research/Piano/test/222/222/mri
\n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz \n
\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
Darwin medical613-6.tau.ac.il<http://medical613-6.tau.ac.il/> 18.2.0 Darwin 
Kernel Version 18.2.0: Fri Oct  5 19:41:49 PDT 2018; 
root:xnu-4903.221.2~2/RELEASE_X86_64 x86_64

recon-all -s 222 exited with ERRORS at Sun Dec 23 15:50:23 IST 2018
***

the information in the talairach_avi.log is as follows:

***
dyld: Symbol not found: ___keymgr_global
  Referenced from: /Applications/freesurfer/bin/gauss_4dfp
  Expected in: /usr/lib/libSystem.B.dylib
 in /Applications/freesurfer/bin/gauss_4dfp
Abort
ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134
ERROR: mpr2mni305 execution aborted
***

to be clear, this -  /usr/lib/libSystem.B.dylib exists exactly where is was 
expected...

the input image, orig.mgz, looks fine and is in 1 mm res...
so im having trouble getting to the bottom of the error.

thanks in advance,
Shachar


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email i

Re: [Freesurfer] problem using recon-all

[Glasser, Matthew]

External Email - Use Caution

This is a known issue with this version of FreeSurfer and newer Ubuntu OS.  We 
hope to have a version of the HCP Pipelines compatible with FreeSurfer 6.0+ in 
the coming weeks.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, January 13, 2019 at 9:46 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] problem using recon-all


External Email - Use Caution

hello,
I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on 
ubuntu, and I encounter this error (copying from the recon-all.log)
___
#@# Talairach Sun Jan 13 17:35:07 IST 2019
/home/shachar/piano_hcp/102/102/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz

Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08 IST 2019 
___

i'm a bit confused by the lack of error descriptions, and would appreciate any 
leads for solving it :)

Shachar


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] problem using recon-all

[Glasser, Matthew]

External Email - Use Caution

Ubuntu 14.04 should still work.

Matt.

From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, January 14, 2019 at 5:43 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>, Matt 
Glasser mailto:glass...@wustl.edu>>, Ido Tavor 
mailto:idota...@gmail.com>>
Subject: Re: problem using recon-all

if the problem is with the versions, maybe downgrading my OS for now will do 
the trick? do you happen know what is the latest ubuntu that is compatible with 
the 5.3-HCP version?
does this also occur in centOS?

thanks

On Sun, 13 Jan 2019 at 17:46 Shachar Gal 
mailto:gal.shac...@gmail.com>> wrote:
hello,
I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on 
ubuntu, and I encounter this error (copying from the recon-all.log)
___
#@# Talairach Sun Jan 13 17:35:07 IST 2019
/home/shachar/piano_hcp/102/102/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz

Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08 IST 2019 
___

i'm a bit confused by the lack of error descriptions, and would appreciate any 
leads for solving it :)

Shachar


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)

[Glasser, Matthew]

External Email - Use Caution

Isn¹t this what GIFTI is for?  PALM and FreeSurfer can use GIFTI.

Matt.

On 1/30/19, 9:17 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

>Hi Dan
>
>sorry, I'm not really sure what you are asking. Doug implemented a
>work-around for nifti in which it breaks up the number of vertices into
>multiple dimensions (to get around the 16-bit dimensions in nifti, which
>was a crazy design decision). freeview detects this and displays them
>appropriately
>
>cheers
>Bruce
>
>
>On Wed, 30 Jan 2019, Daniel
>Leopold wrote:
>
>>
>> External Email - Use Caution
>>
>> Hi Bruce,
>>
>> Chris Rorden informed me that Surfice previously assumed that MGZ/MGH
>>files were voxelwise images used to
>> surface-paint a mesh. Anderson's palm, however, uses the format as a
>>one-to-one correspondence with the vertices
>> (i.e., data-per-vertex). Chris' newest/upcoming version of Surfice
>>automatically detects this data-per-vertex
>> format and can load the files appropriately.
>>
>> The main feature that freeview lacks is the ability to display multiple
>>overlays/sets of palm results at once. My
>> initial approach was to convert the .mgz palm outputs into .nii so that
>>I could use fslmaths to combine results,
>> but (apparently) NIFTI handles a maximum of 65,535 voxels in any one
>>dimension, which is why Chris thought Anderson
>> used MGH, which allows billions of vertices (32-bit).
>>
>> So, Surfice can now load the palm .mgz outputs onto ?h.inflated, .pial,
>>and .curv surfaces, but I'm now wondering
>> if mgh/mgz overlays be be loaded on top of other background meshes
>>(such as BrainMesh_ICBM152 or mni2fs meshes that
>> are provided with Surfice). I've emailed Darren Price because I'm
>>essentially looking for the inverse transform of
>> his mni2fs package (i.e., fs2mni), but I was wondering if you or Doug
>>have encountered this question or similar
>> requests to convert freesurfer to mni surfaces/meshes before? I'm
>>familiar with the Freesurfer Coordinate Systems
>> info, but I don't know how I might generalize the RAS to MNI152 point
>>conversion to an entire surface.
>>
>>
>> Thank you again for your suggestions and help!
>> Dan
>>



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Re: [Freesurfer] problem using recon-all

[Glasser, Matthew]

External Email - Use Caution

There is a little more testing we are doing.

Matt.

From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, February 4, 2019 at 3:32 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>, Ido 
Tavor mailto:idota...@gmail.com>>
Subject: Re: problem using recon-all

hey,
is there any update regarding the release of the FreeSurfer 6 HCP-compatible 
version?

cheers,
Shachar

On Mon, 14 Jan 2019 at 14:58 Shachar Gal 
mailto:gal.shac...@gmail.com>> wrote:
thanks,
hope it'll work
anyway, looking forward for the version 6 release

cheers,
Shachar

On Mon, 14 Jan 2019 at 14:08 Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
Ubuntu 14.04 should still work.

Matt.

From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, January 14, 2019 at 5:43 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>, Matt 
Glasser mailto:glass...@wustl.edu>>, Ido Tavor 
mailto:idota...@gmail.com>>
Subject: Re: problem using recon-all

if the problem is with the versions, maybe downgrading my OS for now will do 
the trick? do you happen know what is the latest ubuntu that is compatible with 
the 5.3-HCP version?
does this also occur in centOS?

thanks

On Sun, 13 Jan 2019 at 17:46 Shachar Gal 
mailto:gal.shac...@gmail.com>> wrote:
hello,
I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on 
ubuntu, and I encounter this error (copying from the recon-all.log)
___
#@# Talairach Sun Jan 13 17:35:07 IST 2019
/home/shachar/piano_hcp/102/102/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz

Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08 IST 2019 
___

i'm a bit confused by the lack of error descriptions, and would appreciate any 
leads for solving it :)

Shachar


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
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Re: [Freesurfer] problem using recon-all

[Glasser, Matthew]

External Email - Use Caution

Several things:

1) The FreeSurfer list is probably not the best place for support for the
HCP Pipelines as there is a dedicated user list
hcp-us...@humanconnectome.org for this.  Folks who support the HCP
Pipelines may not monitor the FreeSurfer list as closely.
2) It is very difficult to follow these threads across multiple days when
the prior replies are not included in each e-mail.
3) it is correct that PreFreeSurfer does not use matlab.  It does use
python however, which you have gotten a bunch of python errors.  It would
appear that there is some incompatibility between Python and your mac¹s
installed libraries, which is used for gradient nonlinearity correction
and several FSL scripts.  Because of how your libraries are configured, it
appears to be looking for them in your matlab install, rather than in your
system libraries folders.  This library
"/Applications/MATLAB_R2017b.app/sys/os/maci64/libgfortran.3.dylib² is not
compatible with your scipy python 3.6 install.  Perhaps there is another
version of libgfortran.3 and you have defaulted your system to look for
this in matlab¹s folders before anywhere else.  This could occur if trying
to run the HCP Pipelines from inside matlab, which is not recommended.

Based on the above, you might get actually best get help on the FSL list
for this specific issue (entitled something like ³cannot run FSL python
code like /usr/local/fsl/bin/imcp on my mac, please see these errors
below²).

Matt.

On 2/17/19, 3:20 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Shachar Gal"  wrote:

>External Email - Use Caution
>
>Actually Im not really sure why Matlab pops up here.. this is ran there
>is nothing that is Matlab dependent in the PreFreesurfer Pipeline...
>
>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



The materials in this message are private and may contain Protected Healthcare 
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Re: [Freesurfer] Gray matter normalized intensity

[Glasser, Matthew]

External Email - Use Caution

What is the other variable?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Dorothy Sincasto mailto:dsinca...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, March 21, 2019 at 8:44 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Gray matter normalized intensity


External Email - Use Caution

Dear Freesurfers

Usually, the mean normalized intensity in aseg.stats is not considered 
important. However, by mistake, I put it in my analysis and found out that the 
mean intensity of the thalamus explains a lot the variance of my data.

What could be the physiological meaning of higher intensity in the thalamus? 
Could it be associated with either increased myelinization ( more axons or 
synapses) or with decreased neural soma? Has anybody reported mean normalized 
intensity effects in subcortical structures?


Thanks
Dorothy



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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: [WARNING: UNSCANNABLE EXTRACTION FAILED]talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***

[Glasser, Matthew]

External Email - Use Caution

He¹s probably got some clinical software that only accepts DICOMs.  While
converting volume files back to DICOMs is possible, I don¹t know if that
is something FreeSurfer supports.  You might need to find another tool to
do that conversion.

Matt.

On 3/25/19, 6:30 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

>I'm not sure what you mean by "what my system will further deal with".
>You
>could extract slices I suppose, but typical MRI acquisitions that are
>highres are volumes. The brainmask.mgz will be volume as will everthing
>else in the mri dir
>
>
>On
>Mon, 25 Mar 2019, Chhavi Yadav wrote:
>
>>
>> External Email - Use Caution
>>
>> ok so after the recon-all command runs, in the output directory's mri
>>folder, a file called
>> brainmask.mgz is formed. I have been doing a freeview -v of this file
>>which corresponds to the final
>> skull stripped output for my input slice that I wanted. Now as per the
>>information that you gave me,
>> I should have a volume.  This leads me to two questions. How do I
>>access the volume, where is it in
>> the folder ? And how to I get slices again from this volume because
>>originally I had slices and
>> slices is what my system will further deal with.
>>
>> On Mon, Mar 25, 2019 at 7:20 PM Bruce Fischl
>> wrote:
>>   there are no outputs for single slices, only for volumes. After we
>>   convert the dicom series everything is a volume from then on, no
>>more
>>   single slices
>>   On Mon, 25 Mar 2019, Chhavi Yadav wrote:
>>
>>   >
>>   > External Email - Use Caution
>>   >
>>   > Okay but then how do I access the mgzs of the rest of the
>>slices? since only one
>>   folder was formed
>>   > which I suppose has the output for a single slice which was
>>mentioned in the recon-all
>>   command with
>>   > -i flag.
>>   >
>>   > On Mon, Mar 25, 2019 at 7:15 PM Bruce Fischl
>> wrote:
>>   >   yes, you don't need to process them separately. We don't
>>in general
>>   >   process slices - we process entire volumes
>>   >
>>   >   cheers
>>   >   Bruce
>>   >   On Mon, 25 Mar 2019, Chhavi Yadav
>>   >   wrote:
>>   >
>>   >   >
>>   >   > External Email - Use Caution
>>   >   >
>>   >   > I meant I want to run autorecon1 over all the slices. I
>>am trying to
>>   preprocess all
>>   >   the slices." If
>>   >   > the rest of the dicoms are in the same dir we
>>   >   > will find them and properly assemble the volume from
>>them." means I dont have
>>   to
>>   >   preprocess all the
>>   >   > slices separately? How do I get the preprocessed mgzs
>>of all the rest of the
>>   slices?
>>   >   >
>>   >   > On Mon, Mar 25, 2019 at 7:08 PM Bruce Fischl
>>
>>   wrote:
>>   >   >   Hi Chhavi
>>   >   >
>>   >   >   can you post this type of question to the FS list
>>(which I'll cc on my
>>   >   >   response)? You only need to give recon-all a
>>single dicom slice that is
>>   >   >   from the correct series. If the rest of the
>>dicoms are in the same dir
>>   we
>>   >   >   will find them and properly assemble the volume
>>from them.
>>   >   >
>>   >   >   cheers
>>   >   >   Bruce
>>   >   >
>>   >   >
>>   >   >   On Mon, 25 Mar 2019, Chhavi Yadav wrote:
>>   >   >
>>   >   >   >
>>   >   >   > External Email - Use Caution
>>   >   >   >
>>   >   >   > Hi Bruce, is there a way I can do recon-all
>>-autorecon1 for all the
>>   slices for
>>   >   a
>>   >   >   subject without
>>   >   >   > using the -i flag? I mean I do not want to
>>mention every single
>>   slice's name
>>   >   in the
>>   >   >   command.
>>   >   >   >
>>   >   >   > On Mon, Mar 25, 2019 at 12:59 PM Bruce Fischl
>>   
>>   >   wrote:
>>   >   >   >
>>   >   >   >   On Mon, 25 Mar 2019, Chhavi Yadav wrote:
>>   >   >   >
>>   >   >   >   >
>>   >   >   >   > External Email - Use Caution
>>
>>   >   >   >   >
>>   >   >   >   > Okay got it. So I will still
>>writerecon-all -autorecon1 -i
>>   new.dcm -s
>>   >   outnew
>>   >   >   >   > Just that new.dcm should be in the
>>folder with the other
>>   slices. Is
>>   >   that
>>   >   >   correct?
>>   >   >   >   >
>>   >   >   >   > Also some of my slices are noisy, just
>>ears or completely
>>   black.
>>   >   >   >   > Sorry for sending to

Re: [Freesurfer] Special image protocol

[Glasser, Matthew]

External Email - Use Caution

No you do not need IV contrast for running FreeSurfer.  Rather it would be
better if that was not done.

Matt.

On 3/27/19, 12:05 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
mustafa amin"  wrote:

>External Email - Use Caution
>
>I am going to use Phillips Achieva 1.5 Tesla by the way. Thank you in
>advance.
>
>Mustafa M. Amin
>Consultant Psychiatrist in Biological Psychiatry
>Department of Psychiatry
>Faculty of Medicine
>Universitas Sumatera Utara
>
>> On 26 Mar 2019, at 21.24, Bruce Fischl 
>>wrote:
>>
>> Hi Mustafa
>>
>> what type of scanner are you using? A normal mprage should be fine.
>> Typically we acquire sagittaly as that is the shortest air-to-air
>> direction. Make sure that the acquisition is 3D and around 1mm
>>isotropic.
>> We may have a protocol you can use depending on your scanner hardware
>>and
>> software
>> cheers
>> Bruce
>>
>>
>>> On Tue, 26 Mar 2019, mustafa amin wrote:
>>>
>>>   External Email - Use Caution
>>>
>>> Dear Douglas,
>>>
>>> I mentioned your suggestion i.e., multiecho mprage at about 1 mm,
>>>however
>>> the radiologist and operator of the MRI did not understand with the
>>>term.
>>> Can you explain it further please? We never done it before, here in
>>>Medan
>>> Indonesia. This is the first time we are going to do it. And, do you
>>>have
>>> suggestion for the MRI slice? Coronal, sagittal or else? Thank you in
>>> advance.
>>>
>>> Yours faithfully,
>>>
>>> Mustafa M. Amin
>>> Consultant Psychiatrist in Biological Psychiatry
>>> Department of Psychiatry
>>> Faculty of Medicine
>>> Universitas Sumatera Utara
>>>
 On 22 Feb 2019, at 00.10, Greve, Douglas N.,Ph.D.
 wrote:

 I highly recommend the multiecho mprage at about 1mm.

> On 2/21/19 10:30 AM, Bruce Fischl wrote:
> Hi Mustafa
>
> FreeSurfer should work fine with many image protocols. If you have
>the
> freedom to choose one, Andre van der Kouwe (ccd) can point you at the
> sequence he developed for Siemens. If you are using a different
>scanner
> give us the details and we can recommend something
>
> cheers
> Bruce
>
>
> On Thu, 21 Feb
> 2019, mustafa amin wrote:
>
>>   External Email - Use Caution
>>
>> Dear member,
>>
>> I am really new with this freesurfer, just need to ask 1 question.
>>Is there a special image protocol before running the MRI and then
>>upload it to freesurfer? Please share your thoughts. Thank you for
>>your kind attention and cooperation.
>>
>> Yours faithfully,
>>
>> Mustafa M. Amin
>> Consultant Psychiatrist in Biological Psychiatry
>> Department of Psychiatry
>> Faculty of Medicine
>> Universitas Sumatera Utara
>>
>>
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>>
>>
>>
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Re: [Freesurfer] Using Custom Atlas for Segmentation of Brain Surfaces

[Glasser, Matthew]

External Email - Use Caution

An updated version of the Power parcellation is available on the FS_LR
atlas mesh in the BALSA database:

https://balsa.wustl.edu/file/show/JX5V

You can run FreeSurfer on your subject¹s T1w images and then either bring
the data onto FS_LR or the atlas onto fsaverage using the instructions
available here:

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uac
t=8&ved=2ahUKEwiOhOXxtsHhAhWBTd8KHXH7CgkQFjAAegQIABAC&url=https%3A%2F%2Fwik
i.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-Free
Surfer-HCP.pdf&usg=AOvVaw2wx1IdlCJFJxczsj8QEw4l

No need to worry about the limitations of MNI space that Bruce mentions.

Matt.

On 4/8/19, 3:40 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

>Hi Mina
>
>I'm not sure about the Power atlas question, but for us the best thing to
>do is stay as close to the scanner data as possible. Ideally dicoms that
>came off the scanner, but alternatively nifti images made from them.
>Transforming to MNI coords will reduce your effective resolution, and
>inverse transforming will reduce it again, so I definitely wouldn't do
>that.
>
>cheers
>Bruce
>  On Mon, 8 Apr 2019, Mina Shire wrote:
>
>>
>> External Email - Use Caution
>>
>> Dear All,
>> I know it is a very basic question but I would really appreciate if I
>>can get any support for source
>> or recommendations about how could I extract custom atlas based surface
>>segmentation using Power et
>> al(2011) atlas please.
>>
>> Thank you very much in advance,
>>
>> Mina
>>
>> On Thu, Apr 4, 2019 at 3:22 PM Mina Shire  wrote:
>>   Dear All,
>> I would like to extract cortical envelop from my subjects T1 images to
>>use later on for a
>> source reconstruction in on their EEG data. I would like to use Power
>>et al (2011)'s atlas
>> with 264 regions. I am pretty new to Freesurfer and my search through
>>the mailing list and
>> tutorials confused me very much. So I would really appreciate if anyone
>>could explain using a
>> custom atlas to me or direct me to the sources that I can follow
>>please.
>>
>> So I have 2 questions regarding that.
>> 1. Is there any chance that you could direct me step by step how to do
>>this with Freesurfer.
>>
>>
>> 2. While I am running extraction with Freesurfer, should I be using ROI
>>nifti files in MNI
>> coordinate or should I be using ROI nifti files that were inverse
>>normalised to subject's
>> native space?
>>
>> I would really appreciate if you could help me with this please.
>>
>> Thank you very much in advance
>>
>> Kind regards
>> Mina
>>
>>



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Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0

[Glasser, Matthew]

External Email - Use Caution

To follow up on this, it seems the issue is related to where the data are 
stored on the user’s server and perhaps the filesystem/mode of access being 
used.  There does not seem to be any issue with Ubuntu generally, as processing 
works fine on the user’s OS drive…

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Jayasekera, Dinal" 
mailto:dinal.jayasek...@wustl.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, April 11, 2019 at 12:11 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0


External Email - Use Caution

Douglas,


I've run the recon-all script with images from patients that were previously 
run using FreeSurfer 5.3.0 and I received the same error.


I haven't run it outside of the HCP pipeline. I can attempt that to see if it 
gives a different result. I'm not exactly sure how to go about doing this. 
Could you advise me on the best sequence of actions to take?


Kind regards,
Dinal Jayasekera

PhD Candidate | InSITE Fellow
Ammar Hawasli Lab
Department of Biomedical Engineering 
| Washington University in St. Louis


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>>
Sent: Wednesday, April 10, 2019 5:27:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0

Have you looked at the images to verify that there are no major problems
with it? Can you run it outside of the HCP pipeline to make sure it is
not an interaction?

On 4/8/19 12:52 PM, Jayasekera, Dinal wrote:
>
> External Email - Use Caution
>
> Dear all,
>
>
> I have been running version 4 of the HCP Pipelines which now used
> FreeSurfer 6.0. I get the following error when running recon-all using
> their FreeSurferPipelineBatch script:
>
>
> /nu_evaluate: crashed while running minc_modify_header (termination
> status=134)/
> /nu_correct: crashed while running nu_evaluate (termination status=65280)/
> /ERROR: nu_correct/
>
> I didn't get this error previously when running FreeSurfer 5.3.0 on
> the same set of data. Are the MNI tools distributed through FreeSurfer
> 6.0 sensitive to the operating system and its version? Does anyone
> have a record of it working on an Ubuntu 14.04 OS?
>
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
> 2) Platform: Ubuntu 14.04
> 3) recon-all.log: see attached
>
> Kind regards,
>
> *Dinal Jayasekera *
> *
> *
> PhD Candidate | InSITE Fellow 
> Ammar Hawasli Lab 
> Department of Biomedical Engineering
>  | Washington University in
> St. Louis 
>
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Re: [Freesurfer] Geometric distortion

[Glasser, Matthew]

External Email - Use Caution

There are different kinds of geometric distortion that affect your data to 
differing extents.  What kind of MRI data was in your study?

Matt.

From:  on behalf of Martin Juneja 

Reply-To: Freesurfer support list 
Date: Monday, May 13, 2019 at 6:53 PM
To: Freesurfer support list 
Subject: [Freesurfer] Geometric distortion


External Email - Use Caution
Hi experts,

I have following question from one of the reviewers regarding recon-all 
pipeline:
"Was geometric distortion corrected? If not, this should be discussed or 
mentioned in the study limitation."
I was wondering if the reviewer is referring to following step in the recon-all 
pipeline. Could you please help me in addressing this concern by the reviewer?

Thanks.
MJ
Cortical Parcellation (-cortparc, -cortparc2)
Assigns a neuroanatomical label to each location on the cortical surface. 
Incorporates both geometric information derived from the cortical model (sulcus 
and curvature), and neuroanatomical convention. Calls mris_ca_label. -cortparc 
creates label/?h.aparc.annot, and -cortparc2 creates 
/label/?h.aparc.a2005s.annot.


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Re: [Freesurfer] Geometric distortion

[Glasser, Matthew]

External Email - Use Caution

For most scanners, gradient nonlinearity correction is a relatively small 
effect that is most prominent in the periphery of the FOV (it is a bit larger 
in the HCP custom scanner because of design constraints).  For 3D structural 
images (e.g. T1w, T2w, FLAIR) there is a small amount of distortion in the 
readout direction as well.  Both of these effects are much smaller than the 
distortion in the phase encoding direction of EPI images, which should always 
be corrected for.

Matt.

On 5/14/19, 4:59 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Martin Reuter"  wrote:

Hi Martin,

probably the reviewer does not mean anything related to FS. Rather,
there is distortion during image acquisition (e.g. gradient non-
linearities). The reviewer probably wants to know if gradient
unwarparing was done prior to running FS. That is why Matthew asked
what MRI data was collected exactly (sequence, scanner etc).

Best, Martin

On Mon, 2019-05-13 at 21:06 -0700, Martin Juneja wrote:
> External Email - Use Caution
> Thank you Matthew for your reply.
>
> I just ran recon-all to get cortical thickness, area and volume
> values for specific ROIs using the steps here:
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
> and correlated the morphometric values with behavioral data.
> I am not sure how can I address reviewer's comment.
>
> Any help would be really appreciated.
>
> On Mon, May 13, 2019 at 5:41 PM Glasser, Matthew 
> wrote:
> > External Email - Use Caution
> > There are different kinds of geometric distortion that affect your
> > data to differing extents.  What kind of MRI data was in your
> > study?
> >
> > Matt.
> >
> > From:  on behalf of Martin
> > Juneja 
> > Reply-To: Freesurfer support list 
> > Date: Monday, May 13, 2019 at 6:53 PM
> > To: Freesurfer support list 
> > Subject: [Freesurfer] Geometric distortion
> >
> > External Email - Use Caution
> > Hi experts,
> >
> > I have following question from one of the reviewers regarding
> > recon-all pipeline:
> > "Was geometric distortion corrected? If not, this should be
> > discussed or mentioned in the study limitation."
> > I was wondering if the reviewer is referring to following step in
> > the recon-all pipeline. Could you please help me in addressing this
> > concern by the reviewer?
> >
> > Thanks.
> > MJ
> > Cortical Parcellation (-cortparc, -cortparc2)
> > Assigns a neuroanatomical label to each location on the cortical
> > surface. Incorporates both geometric information derived from the
> > cortical model (sulcus and curvature), and neuroanatomical
> > convention. Calls mris_ca_label. -cortparc creates
> > label/?h.aparc.annot, and -cortparc2 creates
> > /label/?h.aparc.a2005s.annot.
> >
> > The materials in this message are private and may contain Protected
> > Healthcare Information or other information of a sensitive nature.
> > If you are not the intended recipient, be advised that any
> > unauthorized use, disclosure, copying or the taking of any action
> > in reliance on the contents of this information is strictly
> > prohibited. If you have received this email in error, please
> > immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] T2/Flair benefits in freesurfer 6.0

[Glasser, Matthew]

External Email - Use Caution

Higher the better resolution, but it's particularly important that the 
resolution is close to 3D isotropic for surface reconstruction.

Matt.

On 6/7/19, 1:38 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Jones, Richard"  wrote:

External Email - Use Caution

A few more questions regarding the use of a FLAIR image.

1)If one is using the hires option on T1 images acquired with 
sub-millimeter spatial resolution then, to get the best results with the FLAIR 
option, is matching spatial resolution required for the FLAIR sequence?

2)In a post some time ago 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51413.html) you 
said "V6 was not meant for T2/FLAIR and we didn't test it extensively. We  have 
been optimizing things in the past week for T2/FLAIR and I expect 6.1 will be 
better for them". Are the changes you were referring to incorporated in the 
current development version?

3)Are then any plans to use the FLAIR for multi-modal segmentation in order 
to refine the segmentation of the Pallidium and Putamen, and to possibly 
segment structures such as the substantia nigra and red nucleus?

Thanks,

Richard

Date: Tue, 4 Jun 2019 12:41:51 -0400 (EDT)
From: Bruce Fischl 
Subject: Re: [Freesurfer] T2/Flair benefits in freesurfer 6.0
To: Freesurfer support list 
Message-ID:

Content-Type: text/plain; charset="utf-8"

Hi Aaron

yes, it helps in other situations like blood vessels

cheers
Bruce
On Tue, 4 Jun 2019,
Aaron Tanenbaum wrote:

>
> External Email - Use Caution
>
> I am not too sure if I have asked you this question before. I know the use
> of a flair or T2 helps with dealing with the dura. I was wondering if 
there
> are other benefits??
>
>




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Re: [Freesurfer] Recon-all taking 20 hours to run.

[Glasser, Matthew]

External Email - Use Caution

Most likely some subjects had more topology errors that required correcting.

Matt.

On 6/13/19, 12:05 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tim 
Schäfer"  
wrote:

External Email - Use Caution

Hi Aaron,

I think there are time stamps in the log file, so you should be able to see 
what part of the pipeline took so long.

If you still have one of the log files, could you attach it?

Best,

Tim

> On June 13, 2019 at 6:23 PM Aaron Tanenbaum  
wrote:
>
>
> External Email - Use Caution
>
> I ran 38 subjects through Freesurfer 6.0 on a supercomputer here at Washu.
> The super computer is about 3 years old. Of those 38 subjects, 7 exceeded
> 20 hour time limit on the batch script.  The others took about 12 hours to
> finish. All subjects had a 1mm isotropic MPRAGE and FLAIR. Below is the
> command I used for one of them. Is there a reason for some subjects
> recon-all would take more then 20 hours?
>
>
> recon-all -s 10016_20170414 -i
> /scratch/brierm/Images/10016_20170414_T1.nii -FLAIR
> /scratch/brierm/Images/10016_20170414_FLAIR.nii  -FLAIRpial -all
> -mprage -hippocampal-subfields-T1 -qcache
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and 
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] c_ras for HCP compatibility

[Glasser, Matthew]

External Email - Use Caution

Were the images acquired with the animal in a funny position relative to 
humans?  That might be the issue.  I would convert DICOMs to NIFTI prior to 
FreeSurfer, make sure the image is oriented as RPI or LPI and that the labels 
match the brain (e.g. in a tool like FSLView) and then run FreeSurfer.

Matt.

From:  on behalf of Robert Austin Bruce 
Benn 
Reply-To: Freesurfer support list 
Date: Friday, September 13, 2019 at 7:06 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] c_ras for HCP compatibility


External Email - Use Caution
Hi Y’all,

I was wondering if Y’all could tell me how c_ras is calculated in the x_form 
matrix for orig.mgz?

I’ve been using some animal brains, and the pipeline works very well at 
creating surfaces and aligning them to their coresponding image for freeview.
Post pipeline I’ve been applying the cras matix as derived from the orig.mgz to 
remove the offset for use in wb_view.

The commands for applying the transforms work fine.
However I end up getting a surface that is either inverted, or perpendicular to 
the nifti volume in wb_view.

The animal image does have a large field of view, with a relatively small brain.
I think the cras matrix isn’t getting calculated correctly, but that the images 
I’m using may not have a standered cras so I may need to hack around that.

Could you explain to me how c_ras is calculated?
Also if I need to edit c_ras how would I go about doing it? is it derived from 
the q and s forms?

thanks!

austin

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Re: [Freesurfer] Obtaining MNI Coordinates for HCP annotations

[Glasser, Matthew]

External Email - Use Caution

I'll note that we don't recommend trying to represent cortical areas in general 
as single coordinates. We describe the issues with MNI space group average 
volume alignment in this publication, which illustrates what happens to the 
HCP's cortical areas using different alignment methods:

https://www.pnas.org/content/115/27/E6356.short

Matt.

On 9/19/19, 10:09 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Greve, Douglas N.,Ph.D."  wrote:

What space are they in? Typically, I tell people to run recon-all on the
mni152 volume, then map labels into that subject, then compute coords

On 9/13/19 3:00 PM, Dev vasu wrote:
>
> External Email - Use Caution
>
> Dear all,
>
> I would like to obtain MNI coordinates for HCP annotations , i have
> annotation files for both lh and rh ( which are attached ) , i would
> like to obtain MNI coordinates for them .
>
> I was going through the post
> 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2015-November/042446.html
> , but i could not get a better understanding on how to generate MNI
> values for each label in annot files , that i would like to use for
> graphical analysis.
>
>
> Thanks
> Vasudev
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] ECC or non-ECC Memory?

[Glasser, Matthew]

External Email - Use Caution

If you use non-ECC memory, it is a good idea to run something like memtest86 to 
ensure that it is error free (and return any sticks with errors to the 
manufacturer).  ECC and non-ECC RAM should be similar assuming the non-ECC RAM 
doesn’t have errors 😉

Matt.

From:  on behalf of Sotiris Michos 

Reply-To: Freesurfer support list 
Date: Sunday, October 6, 2019 at 3:01 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] ECC or non-ECC Memory?


External Email - Use Caution
Dear Freesurfer community,

I am interested in building a PC with the goal of running Freesurfer (about 
2000-2500 Euros). I have carefully read 
this very 
informative webpage. However, I still have some questions and I would be glad 
if some assistance could be provided.

I suspect that a proper PC would be placed towards the workstation side of the 
spectrum, since from what I read in the above webpage, Freesurfer can utilize 
multiple cores and is quite demanding in RAM memory per instance.

What I would like to ask is whether ECC Memory is critical for this application 
or if the corruption coming from a non-ECC module has any significant effect on 
the end result. Also, any advice or suggestions about the system's buildup 
would be more than welcome.

Best Regards,
Sotiris Michos


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Re: [Freesurfer] ECC or non-ECC Memory?

[Glasser, Matthew]

External Email - Use Caution

Test your non-ECC memory or use ECC.

Matt.

From:  on behalf of Sotiris Michos 

Reply-To: Freesurfer support list 
Date: Tuesday, October 8, 2019 at 1:48 PM
To: R Edgar 
Cc: Freesurfer support list 
Subject: Re: [Freesurfer] ECC or non-ECC Memory?


External Email - Use Caution
Dear Richard, Matt, fsbuild,

First of all I would like to thank you all for your quite informative answers. 
I am aware of the way ECC memory works, but your answers provided new and 
interesting information.

However, my question is about the criticality of ECC memory specifically for 
Freesurfer. I know for example that for financial computations where high 
precision is required one should use ECC memory while for video encoding tasks 
non-ECC is the memory of choice since the lack of computational accuracy coming 
from non-ECC memory has a minimal (if at all) effect on the end result.

Given that Freesurfer is used for medical-oriented research, is ECC memory 
something that should be required of a system running Freesurfer or its effects 
are not significant according to the experts of the field and your experience?

Regards,
Sotiris Michos

On Tue, 8 Oct 2019 at 02:19, R Edgar 
mailto:freesurfer@gmail.com>> wrote:
On Mon, 7 Oct 2019 at 02:41, fsbuild 
mailto:fsbu...@contbay.com>> wrote:

> For this to work, I think the (hardware) memory controller and the CPU need 
> to support ECC as well.  So if the motherboard you are spec'ing out does not 
> explicitly say it supports ECC, then I would assume it does not.  ECC memory 
> is 2X to 3X more expensive than non-ECC memory. I don't know how motherboard 
> prices compare that do/do not support ECC.  Users who are building machines 
> for supper fast gaming, or audio/video production and streaming typically 
> won't spend extra money on ECC as they want to max out on the CPU, memory, 
> and buss/bandwidth.

I'm not sure about the AMD side, but for Intel you generally have to
go to Xeon chips and motherboards to get ECC support. See the "memory"
section under:
https://www.intel.com/content/www/us/en/support/articles/06778/processors.html
ECC will in general be (slightly) slower than 'regular' RAM due to the
extra parity bits.

HTH,

Richard


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[Freesurfer] FW: Mapping coordinates from sphere file to ?h.white

[Glasser, Matthew]

External Email - Use Caution



From: Timothy Coalson 
Reply-To: Timothy Coalson 
Date: Monday, October 28, 2019 at 8:21 PM
To: "Glasser, Matthew" 
Subject: Re: FW: [Freesurfer] Mapping coordinates from sphere file to ?h.white

That is not a sphere of fs_LR coordinates (in fact, "fs_LR coordinates" is not 
really a meaningful phrase).  That sphere's per-vertex coordinates are 
specifically intended to spatially line up our fs_LR atlas data to fsaverage 
atlas data on the fsaverage atlas sphere, because this is the information 
needed to resample between the atlases.  It has the same number of vertices as 
fs_LR surfaces because it needs to know the target location on the fsaverage 
atlas sphere for every fs_LR vertex.

The inflation of an anatomical surface to a sphere is a tricky process, as the 
surface can easily fold back over itself (which would encode a non-invertible 
transformation).  The path the vertices took to get to a sphere is neither 
recorded, nor particularly important to anyone not working on the 
implementation details of the inflation.  The endpoint of the process, the 
spherical surface, is the only goal, the displacement vectors between them are 
not useful to surface operations (since the data is tied to the vertices, and 
all the vertices still exist in the sphere (just at new coordinates), it is 
trivial to use the same data "on" either the sphere or anatomical surfaces).  
These spherical surfaces are only used to do registration and resampling (which 
does not involve any kind of warp of anatomical coordinates), after which the 
data is used with anatomical surfaces (which always maintain the original shape 
and size even when resampled), because spatial processing should be done on 
brain-shaped geometry, not on spheres.

It is unclear to me what you intend to use the surface you described for, and I 
don't know what the .x5 format is.  The surface resampling weights are fairly 
easily derived from the correct pair of spheres, and resampling does not 
involve any kind of spatial displacement.

Tim

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Oscar Esteban mailto:p...@oscaresteban.es>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, October 28, 2019 at 6:58 PM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Mapping coordinates from sphere file to ?h.white


External Email - Use Caution
Dear experts,

In the context of the BIDS transforms extension and the ".x5" format we chatted 
about in the workshop we made in March at MIT, we are addressing the following 
question.

We have a sphere of fsLR coordinates in fsaverage space (e.g., 
https://github.com/Washington-University/HCPpipelines/blob/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.59k_fs_LR.surf.gii
 - but the question extends to the right hemisphere and also resolutions other 
than 59k).
We want to expand this sphere to the fsaverage's white surface (lh.white, in 
this example). Since coordinates on the fsLR sphere don't match any of 
fsaverage{,3,4,5,6}'s coordinates, we wonder whether FreeSurfer stores 
somewhere/somehow the analytical transform of this mapping.
In other words, how one would map arbitrary coordinates on the surface to a 
particular fsaverage's white (or midthickness, or pial, etc.) surface.

Otherwise, I guess I would pick fsaverage's surfaces (i.e., 7th degree 
icosahedron), and interpolate the displacement vectors that start at each 
sample on the surface and end at the corresponding location of that vertex 
index of the destination surface (lh.white for the example above).

Is there any tool that actually does the _inverse transform of the 
surface-to-sphere mapping_?

Thanks very much.

Regards,
Oscar

--
___
Oscar Esteban, Ph.D.
Postdoctoral Fellow, Poldrack Lab
Stanford University

+1 (650) 733 33 82


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Re: [Freesurfer] Noise reduction + Eddy current reduction

[Glasser, Matthew]

External Email - Use Caution

In general these days the more recent “eddy” tool is preferred for eddy current 
correction of diffusion data.

Matt.

From:  on behalf of "Greve, Douglas 
N.,Ph.D." 
Reply-To: Freesurfer support list 
Date: Saturday, January 11, 2020 at 2:54 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Noise reduction + Eddy current reduction

No, I've always used FSL's eddy_correct
On 1/11/2020 2:17 AM, Adam Rytina wrote:

External Email - Use Caution
Hi Greve,

thanks for your answer. I will try ANTS DenoiseImage.

Regarding Eddy Current - moreover, i have to reduce the eddy current on DWI 
images. Does Freesurfer enable to perform the eddy current reduction?

Thanks a lot
Regards
Adam


Od: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 za uživatele Greve, Douglas N.,Ph.D. 

Odesláno: sobota 11. ledna 2020 0:03
Komu: freesurfer@nmr.mgh.harvard.edu 

Předmět: Re: [Freesurfer] Noise reduction + Eddy current reduction

We don't have anything to denoise. You can try using ANTS DenoiseImage, but 
using on the input might change where the surface is placed. We are 
experimenting with using it inside the stream in a place where it is less 
likely to bias the surface placement.

I don't understand the eddy current question as there should not be eddy 
currents in a typical T1 or FLAIR
On 1/10/2020 2:53 PM, Adam Rytina wrote:

External Email - Use Caution
Hello all,

I want to apply the denoising and eddy current reduction on input images 3DT1 
and 3D Flair. Are there any algorithms in Freesurfer to perform the noise and 
eddy current reduction? Does recon-all involve denoising and eddy current 
reduction? If so, in which processing stage?

Thanks a lot
Regards
Adam



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Re: [Freesurfer] Skipping bias field correction

[Glasser, Matthew]

External Email - Use Caution

Why do you want to do that?  FreeSurfer pretty much requires the values to be 
uniform across the brain and be in a specified range to work properly.

Matt.

From:  on behalf of Patrick 

Reply-To: Patrick , Freesurfer support list 

Date: Monday, January 13, 2020 at 5:44 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Skipping bias field correction


External Email - Use Caution
Dear Freesurfer experts,

I am trying to run recon-all but I want to skip bias field estimation and 
correction step. I have tried the following:

1) Run recon-all by specifiying -nonuintensitycor
2) Running recon-all by specifying "motioncor" followed by "talairach" 
(additionally copying "orig" file and renaming it as "nu"

However, in both the cases, it looks like Freesurfer is still running bias 
correction. How can I go about skipping bias field correction?


Thanks and Regards
Patrick


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Re: [Freesurfer] MNI coordinates from Thalamic nuclei

[Glasser, Matthew]

External Email - Use Caution

Why not represent thalamic nuclei as the actual masks?  Thalamic nuclei are not 
single points.

Matt.

From:  on behalf of Corinna Bauer 

Reply-To: Freesurfer support list 
Date: Friday, February 28, 2020 at 9:26 AM
To: Mailing Freesurfer List 
Subject: [Freesurfer] MNI coordinates from Thalamic nuclei


External Email - Use Caution
Hi all,
Is there a way to obtain the MNI coordinates for the thalamic nuclei?

Thanks


Corinna


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Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)

[Glasser, Matthew]

External Email - Use Caution

That is our multi-modal parcellation.  Tim has some instructions to get data 
from the fs_LR mesh to fsaverage in GIFTI format.  Doug perhaps you can say how 
to convert from GIFTI to annot?

Matt.

From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Thursday, May 7, 2020 at 9:59 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)

* External Email - Caution *
what's hcpmmp1?
On 5/7/2020 4:46 AM, pooja prabhu wrote:

External Email - Use Caution
Hai list,
Can I get some insight on how to convert HCPMMP1 to aseg(provided we have 
annotation files) for fsaverage brain?
 For example: for aparc parcellation we use aparc2aseg and get aparc+aseg.mgz.
Similarly I need for HCPMMP1.
Can someone help me with this?
Thank you



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Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)

[Glasser, Matthew]

External Email - Use Caution

Hi  Doug,

Is there a way to convert from GIFTI label to annot?

Matt.

From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Thursday, May 7, 2020 at 12:21 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)

* External Email - Caution *
If you have the annot files in your individual subject's space, then you can 
create a volume in the same way that aparc+aseg.mgz is created. In v6 and 
before, run mri_aparc2aseg. In v7, run mri_surf2volseg. Look in recon-all.log 
to see how it was run to craeate aparc+aseg.mgz and change the command line to 
indicate a different annot and a different output
On 5/7/2020 12:17 PM, pooja prabhu wrote:

External Email - Use Caution
>HCPMMP1 parcellation is multi modal parcellation
>We need the file something like we have for 'aparc' parcellation.
>The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz)
>How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot)


Date: Thu, May 7, 2020 at 2:16 PM
Subject: HCPMMP1 parcellation to aseg (.mgz)
To: mailto:freesurfer@nmr.mgh.harvard.edu>>

Hai list,
>>Can I get some insight on how to convert HCPMMP1 to aseg(provided we have 
>>annotation files) for fsaverage brain?
 >>For example: for aparc parcellation we use aparc2aseg and get aparc+aseg.mgz.
>>Similarly I need for HCPMMP1.
>>Can someone help me with this?
>>Thank you

From: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Timothy Coalson mailto:tsc...@mst.edu>>
Message-ID: 
<29142489-f691-4e6e-a069-f7377d9c7...@wustl.edu<mailto:29142489-f691-4e6e-a069-f7377d9c7...@wustl.edu>>
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

That is our multi-modal parcellation.  Tim has some instructions to get data 
from the fs_LR mesh to fsaverage in GIFTI format.  Doug perhaps you can say how 
to convert from GIFTI to annot?
Matt.



--
Thank You
Pooja Prabhu




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[Freesurfer] FW: HCPMMP1 parcellation to aseg (.mgz)

[Glasser, Matthew]

External Email - Use Caution



From: Timothy Coalson 
Reply-To: Timothy Coalson 
Date: Thursday, May 7, 2020 at 2:30 PM
To: "Glasser, Matthew" 
Cc: Freesurfer support list 
Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)

The way to map data between freesurfer and fs_LR is in faq #9:

https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?

I seem to recall that the colors in the colored version of our MMP atlas ended 
up unique (at least within the hemisphere), so that should remove one hurdle 
from converting to freesurfer format.

Tim


On Thu, May 7, 2020 at 10:01 AM Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
That is our multi-modal parcellation.  Tim has some instructions to get data 
from the fs_LR mesh to fsaverage in GIFTI format.  Doug perhaps you can say how 
to convert from GIFTI to annot?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Douglas N. Greve" 
mailto:dgr...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, May 7, 2020 at 9:59 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)

* External Email - Caution *
what's hcpmmp1?
On 5/7/2020 4:46 AM, pooja prabhu wrote:

External Email - Use Caution
Hai list,
Can I get some insight on how to convert HCPMMP1 to aseg(provided we have 
annotation files) for fsaverage brain?
 For example: for aparc parcellation we use aparc2aseg and get aparc+aseg.mgz.
Similarly I need for HCPMMP1.
Can someone help me with this?
Thank you


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Re: [Freesurfer] Does freesurfer must use 3-D T1

[Glasser, Matthew]

External Email - Use Caution

Given that the cortex folds in all directions, one’s spatial resolution is 
really only as good as one’s resolution along the worst axis.  Thus, it’s best 
to aim for isotropic resolution (or at least not too far from it).

Matt.

From:  on behalf of John 

Reply-To: Freesurfer support list 
Date: Monday, June 1, 2020 at 8:27 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Does freesurfer must use 3-D T1

External Email - Use Caution
Hi teams,
Does freesurfer must use 3-D T1 to calculate cortical thickness?
Thanks







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Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

[Glasser, Matthew]

External Email - Use Caution

What kind of data does one display in an “OVERLAY” file?

Matt.

From:  on behalf of "Katsumi, Yuta" 

Reply-To: Freesurfer support list 
Date: Thursday, June 18, 2020 at 5:43 PM
To: Freesurfer support list 
Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format


Dear FreeSurfer community,

I would like to be able to display OVERLAY files generated in FreeSurfer on a 
surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states 
in their documentation 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
 that any surfaces to be converted to fs_LR need to be in .gii first, but I 
know mris_convert doesn’t take overlay files as input. It would be great if you 
could please let me know how I might be able to achieve this task.

Thanks,
Yuta


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
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Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

[Glasser, Matthew]

External Email - Use Caution

The appropriate GIFTI extension for that would be .func.gii.  What fsaverage# 
space is that?  Hopefully FreeSurfer provides a tool to convert that to GIFTI 
in full resolution fsaverage space and from there we can help you get it to 
CIFTI in fs_LR.

Matt.

From:  on behalf of "Katsumi, Yuta" 

Reply-To: Freesurfer support list 
Date: Thursday, June 18, 2020 at 10:43 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format


Hi Matt,

For instance, I have a statistical map (e.g., showing magnitude of functional 
connectivity at each vertex) that has been computed in 16k fsaverage space that 
I want to display on a fs_LR surface. I was wondering if there’s a way to 
convert this file (which is in .mgh extension now) to .dscalar so it’d be 
CIFTI/wb compatible.

Thanks,
Yuta

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Thursday, June 18, 2020 at 10:37 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format


External Email - Use Caution
What kind of data does one display in an “OVERLAY” file?

Matt.

From:  on behalf of "Katsumi, Yuta" 

Reply-To: Freesurfer support list 
Date: Thursday, June 18, 2020 at 5:43 PM
To: Freesurfer support list 
Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format


Dear FreeSurfer community,

I would like to be able to display OVERLAY files generated in FreeSurfer on a 
surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states 
in their documentation 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
 that any surfaces to be converted to fs_LR need to be in .gii first, but I 
know mris_convert doesn’t take overlay files as input. It would be great if you 
could please let me know how I might be able to achieve this task.

Thanks,
Yuta


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
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Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

[Glasser, Matthew]

External Email - Use Caution

Is GIFTI a legal output type for mri_convert? I though it only could be 
outputted by mris_convert (which does appear to allow .mgh and .gii).

Matt.

On 6/19/20, 8:00 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tim 
Schäfer"  
wrote:

* External Email - Caution *

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the full 162k 
fsaverage mesh, but once you have the full fsaverage version, to convert to 
gifti, just do:

  mri_convert yourfile.mgh yourfile.func.gii

Best,

Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew"  wrote:
>
>
> External Email - Use Caution
>
> The appropriate GIFTI extension for that would be .func.gii.  What 
fsaverage# space is that?  Hopefully FreeSurfer provides a tool to convert that 
to GIFTI in full resolution fsaverage space and from there we can help you get 
it to CIFTI in fs_LR.
>
> Matt.
>
> From:  on behalf of "Katsumi, 
Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:43 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
format
>
>
> Hi Matt,
>
> For instance, I have a statistical map (e.g., showing magnitude of 
functional connectivity at each vertex) that has been computed in 16k fsaverage 
space that I want to display on a fs_LR surface. I was wondering if there’s a 
way to convert this file (which is in .mgh extension now) to .dscalar so it’d 
be CIFTI/wb compatible.
>
> Thanks,
> Yuta
>
> From:  on behalf of "Glasser, 
Matthew" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:37 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
format
>
>
> External Email - Use Caution
> What kind of data does one display in an “OVERLAY” file?
>
> Matt.
>
> From:  on behalf of "Katsumi, 
Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 5:43 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
format
>
>
> Dear FreeSurfer community,
>
> I would like to be able to display OVERLAY files generated in FreeSurfer 
on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team 
states in their documentation 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
 that any surfaces to be converted to fs_LR need to be in .gii first, but I 
know mris_convert doesn’t take overlay files as input. It would be great if you 
could please let me know how I might be able to achieve this task.
>
> Thanks,
> Yuta
>
> 
> The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If you are 
not the intended recipient, be advised that any unauthorized use, disclosure, 
copying or the taking of any action in reliance on the contents of this 
information is strictly prohibited. If you have received this email in error, 
please immediately notify the sender via telephone or return mail.
>
> 
> The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If you are 
not the intended recipient, be advised that any unauthorized use, disclosure, 
copying or the taking of any action in reliance on the contents of this 
information is strictly prohibited. If you have received this email in error, 
please immediately notify the sender via telephone or return mail.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and 
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised tha

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

[Glasser, Matthew]

External Email - Use Caution

After you convert to GIFTI at fsaverage 164k, you can use these instructions to 
get to fs_LR:

 
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwiyj9jetI7qAhWNVs0KHR5gCtEQFjABegQIBBAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI

Matt.

On 6/19/20, 10:04 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Fischl, Bruce"  wrote:

* External Email - Caution *

In general almost all of our binaries will read or write almost all formats 
we support. There are some exceptions to this, but it is generally true

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Katsumi, Yuta
Sent: Friday, June 19, 2020 9:42 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
format

Thanks, Tim and Matt. I made a typo earlier - I meant to say that my 
overlay files are already in full fsaverage space with ~164k vertices.

I also thought that mri_convert doesn’t take .gii as output, but the 
command that Tim suggested below does indeed seem to work.

Thanks,
Yuta


On 6/19/20, 9:05 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Glasser, Matthew"  wrote:

External Email - Use Caution

Is GIFTI a legal output type for mri_convert? I though it only could be 
outputted by mris_convert (which does appear to allow .mgh and .gii).

Matt.

On 6/19/20, 8:00 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Tim Schäfer"  wrote:

* External Email - Caution *

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the 
full 162k fsaverage mesh, but once you have the full fsaverage version, to 
convert to gifti, just do:

  mri_convert yourfile.mgh yourfile.func.gii

Best,

        Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew" 
 wrote:
>
>
> External Email - Use Caution
>
> The appropriate GIFTI extension for that would be .func.gii.  
What fsaverage# space is that?  Hopefully FreeSurfer provides a tool to convert 
that to GIFTI in full resolution fsaverage space and from there we can help you 
get it to CIFTI in fs_LR.
>
> Matt.
>
> From:  on behalf of 
"Katsumi, Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:43 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in 
the HCP format
>
>
> Hi Matt,
>
> For instance, I have a statistical map (e.g., showing magnitude 
of functional connectivity at each vertex) that has been computed in 16k 
fsaverage space that I want to display on a fs_LR surface. I was wondering if 
there’s a way to convert this file (which is in .mgh extension now) to .dscalar 
so it’d be CIFTI/wb compatible.
>
> Thanks,
> Yuta
>
> From:  on behalf of 
"Glasser, Matthew" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:37 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in 
the HCP format
>
>
> External Email - Use Caution
> What kind of data does one display in an “OVERLAY” file?
>
> Matt.
>
> From:  on behalf of 
"Katsumi, Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 5:43 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] Visualization of FreeSurfer overlays in the 
HCP format
>
>
> Dear FreeSurfer community,
>
> I would like to be able to display OVERLAY files generated in 
FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The 
HCP team states in their documentation 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
 that any surfaces to be converted to fs_LR need to be in .gii first, but I 
know mris_convert doesn’t take overlay files as input. It would be great if you 
could please let me know how I might be able to achieve this task.
 

Re: [Freesurfer] Nifti to gifti conversion

[Glasser, Matthew]

External Email - Use Caution

You can use Connectome Workbench’s wb_command -volume-to-surface-mapping 
(recommend using the -ribbon-constrained option with the white and pial 
surfaces).  You can then use wb_command -cifti-create-dense-timeseries to merge 
the two hemispheres and subcortical grey matter data into a CIFTI file.  If you 
want a pipeline that does this for you, the ciftify pipeline 
(https://github.com/edickie/ciftify) might be a good choice if you have already 
done your preprocessing, or you could use the HCP Pipelines to do all of your 
preprocessing.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Wednesday, June 24, 2020 at 7:42 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] Nifti to gifti conversion

External Email - Use Caution
Hi Experts,

I have a set of resting state data in nifti format. I want to get these data 
into gifti format, so I can then convert them into cifti format and run melodic 
ICA. I suspect using mri_vol2surf would do the trick, but I know you need to 
specify which hemisphere you want the projection to take place on. However, I 
wondered if it was possible to do this for both hemisphere, or whether there is 
a command to merge the two hemisphere back together into a single gifti file 
after running vol2surf separately? The command I am currently running is:

Mri_vol2surf –src filtered_func.nii.gz –out resting_surface.gii –srcreg 
partial-to-struct.lta –hemi lh –projfrac 0.5 –out_type gii

Any advice would be great.
Thanks,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University 
webpage
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Nifti to gifti conversion {Disarmed}

[Glasser, Matthew]

External Email - Use Caution

Here is an example of how we do it in the HCP Pipelines: 
https://github.com/Washington-University/HCPpipelines/blob/master/fMRISurface/scripts/RibbonVolumeToSurfaceMapping.sh
 Line 135

You will need to make sure that all your data are NIFTI/GIFTI/CIFTI to use 
wb_command (you can convert to these from FreeSurfer formats using mri_convert 
and mris_convert).

That said, what is the reason to keep the data super upsampled to FreeSurfer’s 
original irregular mesh?  The 32k standard mesh we usually use has an average 
vertex spacing of 2mm.  We also have a 59k mesh with an average vertex spacing 
of 1.6mm, but have not yet shown that this has advantages.  Particularly since 
you said on the FSL list you plan to smooth the data, I would just use the 
standard mesh outputs.  The HCP Pipelines (and possibly ciftify) produce 
surfaces in both MNI space and the subject’s physical (undeformed) space on 
standard meshes.  Keep in mind that the volume space and surface mesh are 
independent of each other, and one can have standard meshes in subject’s 
physical space and FreeSurfer original meshes in MNI space.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Wednesday, June 24, 2020 at 8:27 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}





External Email - Use Caution
Hi Matt,

Thanks for this. I had previously been using cifitfy (a great tool), but I want 
to keep my data in the native T1 surface space, which isn’t possible with 
ciftify, hence me looking for a different way to do this.
I don’t suppose you know of any documentation that shows an example of how to 
run the volume-surface-mapping command correctly (other than 
this<https://www.humanconnectome.org/software/workbench-command/-volume-to-surface-mapping>)?
 I am a little unsure as to what is required for the flags you suggest (also 
unsure if I need to use a -flag before the paths to the data?). I have tired 
the below, but as you can see I get a couple of errors, one of which I believe 
is due to memory.

While running:
/home/masontwells/Documents/Analysis/workbench/bin_linux64/../exe_linux64/wb_command
 -volume-to-surface-mapping 
/home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated
 /home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial

ERROR: NAME OF FILE: movie_t1_space.nii.gz
PATH TO FILE: /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat

Unable to allocate memory for reading the file.
File Size: 3.24 Gigabytes

Note: The amount of memory required to read a data file may be substantially 
larger than the size of the file due to the way the file's data is organized in 
memory or compression of data within the file.



Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Glasser, Matthew" 

Reply to: Freesurfer support list 
Date: Wednesday, 24 June 2020 at 14:01
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Nifti to gifti conversion


External Email - Use Caution
You can use Connectome Workbench’s wb_command -volume-to-surface-mapping 
(recommend using the -ribbon-constrained option with the white and pial 
surfaces).  You can then use wb_command -cifti-create-dense-timeseries to merge 
the two hemispheres and subcortical grey matter data into a CIFTI file.  If you 
want a pipeline that does this for you, the ciftify pipeline (MailScanner has 
detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" 
claiming to be 
https://github.com/edickie/ciftify<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fedickie%2Fciftify&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7C6bb64a6ce56140a8fa5808d8183eb1ab%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637286004836544062&sdata=aQvX1V%2FJTKoPBFy0mCmduWA6ZuDNfcwjjFYQgIhuFJ8%3D&reserved=0>)
 might be a good choic

Re: [Freesurfer] Nifti to gifti conversion {Disarmed}

[Glasser, Matthew]

External Email - Use Caution

I see, our (Connectome Workbench) border format can be easily resampled to 
different surfaces, but perhaps FreeSurfer’s cannot.  If you do as I suggest 
below, you will be able to make a native mesh CIFTI file.  Doing sICA on that 
will potentially be more computationally intensive than on the original volume 
given the upsampling; however.  I wonder if it would be better to resample the 
sICA maps computed in CIFTI standard space back to the native FreeSurfer mesh 
based on the ciftify output?

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Wednesday, June 24, 2020 at 8:54 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Cc: Erin Dickie 
Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}

External Email - Use Caution
I wanted to keep data in the same space as the subjects surface as I have 
retinotopically defined borders which are on the subjects surface, I want to 
compare these borders to the ICA component on the subjects surface.

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Glasser, Matthew" 

Reply to: Freesurfer support list 
Date: Wednesday, 24 June 2020 at 14:41
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Cc: Erin Dickie 
Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}


External Email - Use Caution
Here is an example of how we do it in the HCP Pipelines: MailScanner has 
detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" 
claiming to be 
https://github.com/Washington-University/HCPpipelines/blob/master/fMRISurface/scripts/RibbonVolumeToSurfaceMapping.sh<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Fblob%2Fmaster%2FfMRISurface%2Fscripts%2FRibbonVolumeToSurfaceMapping.sh&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cbcd1c9e709ea4369700d08d818444244%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637286028746133847&sdata=XF76ow3uBLm%2F0Q0%2FLAdEpdiO1ejg%2FqPcQKYWjDCnaYU%3D&reserved=0>
 Line 135

You will need to make sure that all your data are NIFTI/GIFTI/CIFTI to use 
wb_command (you can convert to these from FreeSurfer formats using mri_convert 
and mris_convert).

That said, what is the reason to keep the data super upsampled to FreeSurfer’s 
original irregular mesh?  The 32k standard mesh we usually use has an average 
vertex spacing of 2mm.  We also have a 59k mesh with an average vertex spacing 
of 1.6mm, but have not yet shown that this has advantages.  Particularly since 
you said on the FSL list you plan to smooth the data, I would just use the 
standard mesh outputs.  The HCP Pipelines (and possibly ciftify) produce 
surfaces in both MNI space and the subject’s physical (undeformed) space on 
standard meshes.  Keep in mind that the volume space and surface mesh are 
independent of each other, and one can have standard meshes in subject’s 
physical space and FreeSurfer original meshes in MNI space.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Wednesday, June 24, 2020 at 8:27 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}





External Email - Use Caution
Hi Matt,

Thanks for this. I had previously been using cifitfy (a great tool), but I want 
to keep my data in the native T1 surface space, which isn’t possible with 
ciftify, hence me looking for a different way to do this.
I don’t suppose you know of any documentation that shows an example of how to 
run the volume-surface-mapping command correctly (other than 
this<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.humanconnectome.org%2Fsoftware%2Fworkbench-command%2F-volume-to-surface-mapping&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cbcd1c9e709ea4369700d08d818444244%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637286028746143838&sdata=vK%2BJfdZzLcG3z1ZQ0cM%2FT6Kb0JrUnBPCLzMvkTv8LLA%3D&reserved=0>)?
 I am a little unsure as to what is required for the flags you suggest (also 
unsure if I need to use a -flag before the paths to the data?). I have tired 
the bel

Re: [Freesurfer] Nifti to gifti conversion {Disarmed}

[Glasser, Matthew]

External Email - Use Caution

Like I said, I would, for computational reasons, recommend using the ciftify 
outputs and then resampling the spatial ICA maps back to the native mesh where 
your borders are.

If you don’t want to do it that way for some reason, do this:

Here is an example of how we do it in the HCP Pipelines: MailScanner has 
detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" 
claiming to be 
https://github.com/Washington-University/HCPpipelines/blob/master/fMRISurface/scripts/RibbonVolumeToSurfaceMapping.sh<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Fblob%2Fmaster%2FfMRISurface%2Fscripts%2FRibbonVolumeToSurfaceMapping.sh&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cfcc952b6a224466d7eea08d818473771%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637286041454570723&sdata=W%2BjnOrI%2BfabRR9E3ty5KY4ODqUMKRzVnJJGEfV%2FrAB8%3D&reserved=0>
 Line 135

You will need to make sure that all your data are NIFTI/GIFTI/CIFTI to use 
wb_command (you can convert to these from FreeSurfer formats using mri_convert 
and mris_convert).

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Wednesday, June 24, 2020 at 9:45 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}



External Email - Use Caution
Hi Matt,

Are you referring to using the volume-to-surface wb command and then using 
create-dense-timeseries to merge the two hemispheres together into a CIFTI 
before running melodic? Can you run this using the freesurfer outputs? E.g. 
using the lh.inflated as the surface and the lh.white and lh.pial as the inner 
and outer surfaces? The metric-out flag, can this just be lh_functional.gii? If 
so, have you any idea what might be causing the error I showed in the previous 
email?

Thanks for your help.
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Glasser, Matthew" 

Reply to: Freesurfer support list 
Date: Wednesday, 24 June 2020 at 15:02
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Cc: Erin Dickie 
Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}


External Email - Use Caution
I see, our (Connectome Workbench) border format can be easily resampled to 
different surfaces, but perhaps FreeSurfer’s cannot.  If you do as I suggest 
below, you will be able to make a native mesh CIFTI file.  Doing sICA on that 
will potentially be more computationally intensive than on the original volume 
given the upsampling; however.  I wonder if it would be better to resample the 
sICA maps computed in CIFTI standard space back to the native FreeSurfer mesh 
based on the ciftify output?

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Wednesday, June 24, 2020 at 8:54 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Cc: Erin Dickie 
Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}

External Email - Use Caution
I wanted to keep data in the same space as the subjects surface as I have 
retinotopically defined borders which are on the subjects surface, I want to 
compare these borders to the ICA component on the subjects surface.

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Glasser, Matthew" 

Reply to: Freesurfer support list 
Date: Wednesday, 24 June 2020 at 14:41
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Cc: Erin Dickie 

Re: [Freesurfer] Nifti to gifti conversion {Disarmed}

[Glasser, Matthew]

External Email - Use Caution

I’m not sure what algorithm mri_vol2surf uses for this purpose and I don’t know 
what level of compatibility there is with CIFTI in FreeSurfer currently.  
Perhaps one of the FreeSurfer developers can comment more on that.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Wednesday, June 24, 2020 at 12:07 PM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}



External Email - Use Caution
Matt,

Just another point. Is it not possible to use mri_vol2surf to project the 
functional data onto the lh and then rh surfaces and then using a second 
command to convert these into a single CIFTI format, such as 
cifti-create-dense-timeseries?

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of Mason Wells 

Reply to: Freesurfer support list 
Date: Wednesday, 24 June 2020 at 15:46
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}


External Email - Use Caution
Hi Matt,

Are you referring to using the volume-to-surface wb command and then using 
create-dense-timeseries to merge the two hemispheres together into a CIFTI 
before running melodic? Can you run this using the freesurfer outputs? E.g. 
using the lh.inflated as the surface and the lh.white and lh.pial as the inner 
and outer surfaces? The metric-out flag, can this just be lh_functional.gii? If 
so, have you any idea what might be causing the error I showed in the previous 
email?

Thanks for your help.
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Glasser, Matthew" 

Reply to: Freesurfer support list 
Date: Wednesday, 24 June 2020 at 15:02
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Cc: Erin Dickie 
Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}


External Email - Use Caution
I see, our (Connectome Workbench) border format can be easily resampled to 
different surfaces, but perhaps FreeSurfer’s cannot.  If you do as I suggest 
below, you will be able to make a native mesh CIFTI file.  Doing sICA on that 
will potentially be more computationally intensive than on the original volume 
given the upsampling; however.  I wonder if it would be better to resample the 
sICA maps computed in CIFTI standard space back to the native FreeSurfer mesh 
based on the ciftify output?

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Wednesday, June 24, 2020 at 8:54 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Cc: Erin Dickie 
Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}

External Email - Use Caution
I wanted to keep data in the same space as the subjects surface as I have 
retinotopically defined borders which are on the subjects surface, I want to 
compare these borders to the ICA component on the subjects surface.

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caer

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Glasser, Matthew]

External Email - Use Caution

Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



External Email - Use Caution
Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii 
format (from FS format)

  *   e.g. mris_convert lh.pial lh.pial.surf.gii
I then applied the transformation to align the filtered_func to the T1

  *   mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta 
--fstarg --o movie_t1_space.nii.gz
I then tried to run the following wb command

  *   wb_command -volume-to-surface-mapping 
/home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated.surf.gii
 /home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white.surf.gii
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial.surf.gii
Which resulted in this subsequent error.

ERROR: NAME OF FILE: movie_t1_space.nii.gz
PATH TO FILE: /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat

Unable to allocate memory for reading the file.

File Size: 3.24 Gigabytes

Note: The amount of memory required to read a data file may be substantially 
larger than the size of the file due to the way the file's data is organized in 
memory or compression of data within the file.

Any advice on how to convert NIFTI to GIFTI and then GIFTI to CIFTI whilst 
keeping the data in the subjects space would be really appreciated.

Best wishes,
Mason


Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University 
webpage
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Glasser, Matthew]

External Email - Use Caution

Scratch that, I guess you did include a surface.  How much RAM do you have 
available and are you on a 64bit OS?  As I mentioned last week, what you are 
trying to do is not computationally efficient and not really the best approach 
to go about things.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:24 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



External Email - Use Caution
Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii 
format (from FS format)

  *   e.g. mris_convert lh.pial lh.pial.surf.gii
I then applied the transformation to align the filtered_func to the T1

  *   mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta 
--fstarg --o movie_t1_space.nii.gz
I then tried to run the following wb command

  *   wb_command -volume-to-surface-mapping 
/home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated.surf.gii
 /home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white.surf.gii
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial.surf.gii
Which resulted in this subsequent error.

ERROR: NAME OF FILE: movie_t1_space.nii.gz
PATH TO FILE: /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat

Unable to allocate memory for reading the file.

File Size: 3.24 Gigabytes

Note: The amount of memory required to read a data file may be substantially 
larger than the size of the file due to the way the file's data is organized in 
memory or compression of data within the file.

Any advice on how to convert NIFTI to GIFTI and then GIFTI to CIFTI whilst 
keeping the data in the subjects space would be really appreciated.

Best wishes,
Mason


Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that an

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Glasser, Matthew]

External Email - Use Caution

Yes you are probably low on memory (3.5GB is really low for brain imaging these 
days).  Like I said, probably best to use the ciftify outputs if you have them 
and then resample the ICA maps back to the native mesh.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 12:50 PM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Hi Matt,

I have 3.5GB free on my 64 bit linux machine, do you think the wb_command issue 
is due to memory alone then? Perhaps I misunderstood your previous emails about 
this, I thought that using the workbench commands was the best way. E.g. 
running volume-to-surface to get the functional data resampled to the subjects 
lh and rh surface, and then cifti-create-dense-timerseries to create a a single 
cifti file with the functional data on the subjects surface? Then I was going 
to use the matlab code you suggest to get an estimation of dimensionality and 
finally run melodic. Is this not the best route to go down with my aims in 
mind? This was also why I asked the FS list whether the same thing can be done 
with mri_vol2surf or other FS commands.

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Glasser, Matthew" 

Reply to: Freesurfer support list 
Date: Monday, 29 June 2020 at 17:28
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion


External Email - Use Caution
Scratch that, I guess you did include a surface.  How much RAM do you have 
available and are you on a 64bit OS?  As I mentioned last week, what you are 
trying to do is not computationally efficient and not really the best approach 
to go about things.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:24 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



External Email - Use Caution
Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii 
format (from FS format)

  *   e.g. mris_convert lh.pial lh.pial.surf.gii
I then applied the transformation to align the filtered_func to the T1

  *   mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta 
--fstarg --o movie_t1_space.nii.gz
I then tried to run the following wb command

  *   wb_command -volume-to-surface-mapping 
/home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz
 
/home/masontwells/Documents/Data/freesurfer/subj

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Glasser, Matthew]

External Email - Use Caution

Also I missed that you upsampled the volume fMRI file massively as well.  
Indeed, this is not how I would recommend going about things, particularly in a 
memory limited environment.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 1:11 PM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Yes you are probably low on memory (3.5GB is really low for brain imaging these 
days).  Like I said, probably best to use the ciftify outputs if you have them 
and then resample the ICA maps back to the native mesh.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 12:50 PM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Hi Matt,

I have 3.5GB free on my 64 bit linux machine, do you think the wb_command issue 
is due to memory alone then? Perhaps I misunderstood your previous emails about 
this, I thought that using the workbench commands was the best way. E.g. 
running volume-to-surface to get the functional data resampled to the subjects 
lh and rh surface, and then cifti-create-dense-timerseries to create a a single 
cifti file with the functional data on the subjects surface? Then I was going 
to use the matlab code you suggest to get an estimation of dimensionality and 
finally run melodic. Is this not the best route to go down with my aims in 
mind? This was also why I asked the FS list whether the same thing can be done 
with mri_vol2surf or other FS commands.

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Glasser, Matthew" 

Reply to: Freesurfer support list 
Date: Monday, 29 June 2020 at 17:28
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion


External Email - Use Caution
Scratch that, I guess you did include a surface.  How much RAM do you have 
available and are you on a 64bit OS?  As I mentioned last week, what you are 
trying to do is not computationally efficient and not really the best approach 
to go about things.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:24 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



External Email - Use Caution
Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf

Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

[Glasser, Matthew]

External Email - Use Caution

I would find using something like ciftify (https://github.com/edickie/ciftify) 
potentially more straightforward (and then you can just use wb_command 
-cifti-parcellate on 
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
  It is possible to go the other direction too (e.g. using this link: 
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
 and then perhaps someone on the list can explain how to go from GIFTI on 
fsaverage to .annot on the native meshes and extract the stats.

Matt.

On 7/14/20, 8:54 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Alina Rojas"  wrote:

* External Email - Caution *

External Email - Use Caution

Hello Freesurfer support list,

I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my 
subjects to get the values of the parcellation, like aparc.stats but aparc 
being HCP-MMP1. The aim ist to compare the cortical thickness of the 
Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the 
archive and didn’t find the solution. It would be so great if you could help me!

Thank you and regards,

Alina Rojas

___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

[Glasser, Matthew]

External Email - Use Caution

So how exactly did you make a .gcs without the individual subject parcellations 
or the multi-modal features used for classifying cortical areas?  Note that we 
are working on a tool for folks to do this.

Matt.

From:  on behalf of Álvaro Deleglise 

Reply-To: Freesurfer support list 
Date: Tuesday, July 14, 2020 at 9:49 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats



External Email - Use Caution
Hi Alina and Matthew,
I think there is a simple solution to the problem. You can use the .gcs files 
of the parcellation you are interested in! You have to run the mris_ca_label 
command to apply the parcellation in individual subject space and get de .annot 
files of each hemisphere. Then, you can use mris_anatomical_stats to get the 
.stats files from these annot files. Finally, you can use aparcstats2table to 
get the metrics of your parcellation.

Here's and example:
mris_ca_label -l $SUBJECTS_DIR//label/?h.cortex.label \
   lh $SUBJECTS_DIR//surf/?h.sphere.reg \
  /?h.parcellation_X.gcs \
  $SUBJECTS_DIR//label/?h.parcellation_X.annot

mris_anatomical_stats -th3 -mgz -cortex ../label/?h.cortex.label -f 
stats/?h.parcellation_X.stats -b -a label/?h.parcellation_X.annot -c 
label/aparc.parcellation_X.ctab  ?h

If you want to, I can provide you the .gcs files of the HCP-MMP1-Atlas.


El mar., 14 jul. 2020 a las 11:19, Glasser, Matthew 
(mailto:glass...@wustl.edu>>) escribió:
External Email - Use Caution

I would find using something like ciftify (https://github.com/edickie/ciftify) 
potentially more straightforward (and then you can just use wb_command 
-cifti-parcellate on 
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
  It is possible to go the other direction too (e.g. using this link: 
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
 and then perhaps someone on the list can explain how to go from GIFTI on 
fsaverage to .annot on the native meshes and extract the stats.

Matt.

On 7/14/20, 8:54 AM, 
"freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Alina Rojas" 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of alinacol...@gmail.com<mailto:alinacol...@gmail.com>> wrote:

* External Email - Caution *

External Email - Use Caution

Hello Freesurfer support list,

I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my 
subjects to get the values of the parcellation, like aparc.stats but aparc 
being HCP-MMP1. The aim ist to compare the cortical thickness of the 
Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the 
archive and didn’t find the solution. It would be so great if you could help me!

Thank you and regards,

Alina Rojas

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

[Glasser, Matthew]

External Email - Use Caution

They didn’t have that data either.  So perhaps there is some possibility of a 
.gcs having improved performance over a simple surface registration depending 
on how this was done (e.g. if the MSMAll registration were used to get the 
individual lables and there are “modes” of folding that correlate with “modes” 
of areal size, shape, and positions).  Certainly no one has worked with us on 
actually validating this approach though (e.g. comparing the output of the .gcs 
to the “gold standard” multi-modal areal classifier outputs generated on 
individual subjects).  So I would use with caution.

Matt.

From:  on behalf of Álvaro Deleglise 

Reply-To: Freesurfer support list 
Date: Tuesday, July 14, 2020 at 10:01 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

External Email - Use Caution
I found the .gcs files in a git repo: https://github.com/faskowit/multiAtlasTT

El mar., 14 jul. 2020 a las 11:58, Glasser, Matthew 
(mailto:glass...@wustl.edu>>) escribió:

External Email - Use Caution
So how exactly did you make a .gcs without the individual subject parcellations 
or the multi-modal features used for classifying cortical areas?  Note that we 
are working on a tool for folks to do this.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Álvaro Deleglise 
mailto:alvarodelegl...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, July 14, 2020 at 9:49 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats



External Email - Use Caution
Hi Alina and Matthew,
I think there is a simple solution to the problem. You can use the .gcs files 
of the parcellation you are interested in! You have to run the mris_ca_label 
command to apply the parcellation in individual subject space and get de .annot 
files of each hemisphere. Then, you can use mris_anatomical_stats to get the 
.stats files from these annot files. Finally, you can use aparcstats2table to 
get the metrics of your parcellation.

Here's and example:
mris_ca_label -l $SUBJECTS_DIR//label/?h.cortex.label \
   lh $SUBJECTS_DIR//surf/?h.sphere.reg \
  /?h.parcellation_X.gcs \
  $SUBJECTS_DIR//label/?h.parcellation_X.annot

mris_anatomical_stats -th3 -mgz -cortex ../label/?h.cortex.label -f 
stats/?h.parcellation_X.stats -b -a label/?h.parcellation_X.annot -c 
label/aparc.parcellation_X.ctab  ?h

If you want to, I can provide you the .gcs files of the HCP-MMP1-Atlas.


El mar., 14 jul. 2020 a las 11:19, Glasser, Matthew 
(mailto:glass...@wustl.edu>>) escribió:
External Email - Use Caution

I would find using something like ciftify (https://github.com/edickie/ciftify) 
potentially more straightforward (and then you can just use wb_command 
-cifti-parcellate on 
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
  It is possible to go the other direction too (e.g. using this link: 
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
 and then perhaps someone on the list can explain how to go from GIFTI on 
fsaverage to .annot on the native meshes and extract the stats.

Matt.

On 7/14/20, 8:54 AM, 
"freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Alina Rojas" 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of alinacol...@gmail.com<mailto:alinacol...@gmail.com>> wrote:

* External Email - Caution *

External Email - Use Caution

Hello Freesurfer support list,

I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my 
subjects to get the values of the parcellation, like aparc.stats but aparc 
being HCP-MMP1. The aim ist to compare the cortical thickness of the 
Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the 
archive and didn’t find the solution. It would be so great if you could help me!

Thank you and regards,

Alina Rojas

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in rel

Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

[Glasser, Matthew]

External Email - Use Caution

I would use https://balsa.wustl.edu/file/show/3VLx which is the CIFTI label 
file.  The pscalar is not a label file, but rather the average thicknesses in 
each cortical area.  You can view the average thicknesses in Connectome 
Workbench or print out the results with wb_command -cifti-convert -to-text.

Matt.

From:  on behalf of Alina Rojas 

Reply-To: Freesurfer support list 
Date: Monday, July 20, 2020 at 4:32 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

External Email - Use Caution
Thank you, the ciftify was run successfully! But now I have questions to the 
wb-command -cifti-parcellate:

wb_command -cifti-parcellate

   - the cifti file to parcellate

   - a cifti label file to use for the parcellation

   - which mapping to parcellate (integer, ROW, or COLUMN)

   - output - output cifti file
I understand that   should be 
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii,
 but what should I use as label? The 
Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii 
from https://balsa.wustl.edu/WN56? And the output from the -cifty-parcellate is 
.pscalar.nii..how do I get from there to GIFTI?

And for the GIFTY to .annot I would do:

  mris_convert --annot lh.aparc.gii lh.white.gii lh.aparc.annot (Freesurfer 
example)

Thank you,

Alina

Am 14.07.2020 um 16:17 schrieb Glasser, Matthew 
mailto:glass...@wustl.edu>>:

   External Email - Use Caution

I would find using something like ciftify (https://github.com/edickie/ciftify) 
potentially more straightforward (and then you can just use wb_command 
-cifti-parcellate on 
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
  It is possible to go the other direction too (e.g. using this link: 
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
 and then perhaps someone on the list can explain how to go from GIFTI on 
fsaverage to .annot on the native meshes and extract the stats.

Matt.

On 7/14/20, 8:54 AM, 
"freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Alina Rojas" 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of alinacol...@gmail.com<mailto:alinacol...@gmail.com>> wrote:

   * External Email - Caution *

   External Email - Use Caution

   Hello Freesurfer support list,

   I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my 
subjects to get the values of the parcellation, like aparc.stats but aparc 
being HCP-MMP1. The aim ist to compare the cortical thickness of the 
Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the 
archive and didn’t find the solution. It would be so great if you could help me!

   Thank you and regards,

   Alina Rojas

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Re: [Freesurfer] T2 or FLAIR data to improve pial surfaces

[Glasser, Matthew]

External Email - Use Caution

What is the resolution of these images?

Matt.

From:  on behalf of "Batra, Vinita R." 

Reply-To: Freesurfer support list 
Date: Monday, July 20, 2020 at 11:13 AM
To: Freesurfer support list 
Subject: [Freesurfer] T2 or FLAIR data to improve pial surfaces

External Email - Use Caution
Dear FreeSurfer experts,

I have both T2 and FLAIR images for the majority of the subjects in my study,
and I want to use them to improve pial surface reconstruction during recon-all
as explained in [1].

My questions are:

1) In general, should I prefer FLAIR over T2, or the other way around?
2) Some subjects (< 10%) do not have a FLAIR image, and others do not have a
T2. Do you think that it is fine to use FLAIR for some subjects, and T2 for 
others, in the same study? We will perform manual QC after the recon-all run 
and exclude bad quality images so I wanted to hear your opinion.

Best,

VB



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Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

[Glasser, Matthew]

External Email - Use Caution

wb_command -file-information on the .dlabel.nii file should do the trick.

Matt.

From:  on behalf of Alina Rojas 

Reply-To: Freesurfer support list 
Date: Monday, July 20, 2020 at 6:13 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats



External Email - Use Caution
Thank you for the quick answer! For the archive and my understanding…the 
pscalar gives out a column with 360 values, these values are the average 
thickness of my one subject and finally, the data I was searching for: cortical 
thickness values from my subject obtained with Freesurfer but with the 
parcellation of the HCP-MMP1. Is there a document or a command where I can 
correlate these values with the name/number of cortical area?

Regards,

Alina


Am 20.07.2020 um 11:32 schrieb Alina Rojas 
mailto:alinacol...@gmail.com>>:

Thank you, the ciftify was run successfully! But now I have questions to the 
wb-command -cifti-parcellate:

wb_command -cifti-parcellate

   - the cifti file to parcellate

   - a cifti label file to use for the parcellation

   - which mapping to parcellate (integer, ROW, or COLUMN)

   - output - output cifti file
I understand that   should be 
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii,
 but what should I use as label? The 
Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii 
from https://balsa.wustl.edu/WN56? And the output from the -cifty-parcellate is 
.pscalar.nii..how do I get from there to GIFTI?

And for the GIFTY to .annot I would do:

  mris_convert --annot lh.aparc.gii lh.white.gii lh.aparc.annot (Freesurfer 
example)

Thank you,

Alina

Am 14.07.2020 um 16:17 schrieb Glasser, Matthew 
mailto:glass...@wustl.edu>>:

   External Email - Use Caution

I would find using something like ciftify (https://github.com/edickie/ciftify) 
potentially more straightforward (and then you can just use wb_command 
-cifti-parcellate on 
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
  It is possible to go the other direction too (e.g. using this link: 
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
 and then perhaps someone on the list can explain how to go from GIFTI on 
fsaverage to .annot on the native meshes and extract the stats.

Matt.

On 7/14/20, 8:54 AM, 
"freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Alina Rojas" 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of alinacol...@gmail.com<mailto:alinacol...@gmail.com>> wrote:

   * External Email - Caution *

   External Email - Use Caution

   Hello Freesurfer support list,

   I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my 
subjects to get the values of the parcellation, like aparc.stats but aparc 
being HCP-MMP1. The aim ist to compare the cortical thickness of the 
Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the 
archive and didn’t find the solution. It would be so great if you could help me!

   Thank you and regards,

   Alina Rojas

   ___
   Freesurfer mailing list
   Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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intended recipient, be advised that any unauthorized use, disclosure, copying 
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strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] use of ANTs Denoising in FS 7.1

[Glasser, Matthew]

External Email - Use Caution

Perhaps it smooths the data some and that would impair the gradient placement 
of the final white and pial surfaces?

Matt.

From:  on behalf of "Alexopoulos, 
Dimitrios" 
Reply-To: Freesurfer support list 
Date: Tuesday, August 25, 2020 at 3:56 PM
To: Freesurfer support list 
Subject: [Freesurfer] use of ANTs Denoising in FS 7.1

External Email - Use Caution
Hi all,

In previous datasets, and prior to FS 7, we independently ran ANTs denosing on 
the input T1s prior to running recon-all,
However, FS 7.1 now appears to use the  denosing utility in parts of the 
pipeline.

“ANTS denoise is used when creating the orig surface (but not thefinal 
surfaces)”

Does this mean the denoised image is only used in the segmentation part of the 
pipeline (to generated the aseg.mgz) and does not propagate through to final 
surfaces?  Why not use  denoised T1 through the surface-generation phase of the 
pipeline.

Can you provide some further clarification.

Thx.
Jim





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Re: [Freesurfer] Prescan normalize and freesurfer

[Glasser, Matthew]

External Email - Use Caution

What head coil did you use?  Do you have a highres T2w or FLAIR?

Matt.

From:  on behalf of "Mikolas, Pavol" 

Reply-To: Freesurfer support list 
Date: Thursday, September 17, 2020 at 7:12 AM
To: "'freesurfer@nmr.mgh.harvard.edu'" 
Subject: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution
Dear Freesurfer Developers,

I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using 
Freesurfer. I found out, that most of the scans were performed with the 
‘prescan normalize’ option. However, by approx..  12 % of participants, this 
option is missing. I also have complete data of all participants WITHOUT 
prescan normalize. In this analysis, we are interested in the correlation of GM 
volume in specific ROIs with clinical symptoms. Now we have two options:


  1.  Use the ‘prescan normalize’ dataset and account for the 12% without this 
option as a covariate
  2.  Use the complete dataset without ‘prescan normalize’

It would be very helpful, if you could share your arguments / experience with 
this, so that we proceed in the best manner.

Thank you, best regards

Pavol



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
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Re: [Freesurfer] Prescan normalize and freesurfer

[Glasser, Matthew]

External Email - Use Caution

That alone will be a huge factor in variable SNR (and receive field).  Head 
coils are not interchangeable like that.

Matt.

From:  on behalf of "Mikolas, Pavol" 

Reply-To: Freesurfer support list 
Date: Thursday, September 17, 2020 at 7:22 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution
Dear Matt,

unfortunately we have no highres T2w or FLAIR.
In this multicentric study, we tended to use the 12 head coil. However, some 
centers used a 8 or a 32 head coil.

Thanks

Pavol


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Glasser, Matthew
Gesendet: Donnerstag, 17. September 2020 14:14
An: Freesurfer support list 
Betreff: Re: [Freesurfer] Prescan normalize and freesurfer


External Email - Use Caution
What head coil did you use?  Do you have a highres T2w or FLAIR?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Mikolas, Pavol" 
mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 17, 2020 at 7:12 AM
To: "'freesurfer@nmr.mgh.harvard.edu'" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution
Dear Freesurfer Developers,

I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using 
Freesurfer. I found out, that most of the scans were performed with the 
‘prescan normalize’ option. However, by approx..  12 % of participants, this 
option is missing. I also have complete data of all participants WITHOUT 
prescan normalize. In this analysis, we are interested in the correlation of GM 
volume in specific ROIs with clinical symptoms. Now we have two options:


  1.  Use the ‘prescan normalize’ dataset and account for the 12% without this 
option as a covariate
  2.  Use the complete dataset without ‘prescan normalize’

It would be very helpful, if you could share your arguments / experience with 
this, so that we proceed in the best manner.

Thank you, best regards

Pavol




The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
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Re: [Freesurfer] Prescan normalize and freesurfer

[Glasser, Matthew]

External Email - Use Caution

Maybe Bruce or Doug wants to comment but probably if you are using a 12CH coil 
it isn’t so important to have on.  It’s pretty much required for a 32CH coil, 
as the bias field is quite fast.

Matt.

From:  on behalf of "Mikolas, Pavol" 

Reply-To: Freesurfer support list 
Date: Thursday, September 17, 2020 at 9:02 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] Prescan normalize and freesurfer



External Email - Use Caution
Dear Matthew,

thank you for this important point. I will check this. There might be just a 
few subjects with 8 and 32 head coil, so that it should be possible to discard 
them without affecting the sample size too much.

Do you think, you could give use some general hint to the ‘prescan normalize’ 
option? We cannot guess the benefit for our analysis well. Generally, if the 
benefit is rather low, we would tend to use the data without ‘prescan 
normalize’. What do you think?

Thank you, all best

Pavol


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Glasser, Matthew
Gesendet: Donnerstag, 17. September 2020 15:44
An: Freesurfer support list 
Betreff: Re: [Freesurfer] Prescan normalize and freesurfer


External Email - Use Caution
That alone will be a huge factor in variable SNR (and receive field).  Head 
coils are not interchangeable like that.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Mikolas, Pavol" 
mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 17, 2020 at 7:22 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution
Dear Matt,

unfortunately we have no highres T2w or FLAIR.
In this multicentric study, we tended to use the 12 head coil. However, some 
centers used a 8 or a 32 head coil.

Thanks

Pavol


Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 Im Auftrag von Glasser, Matthew
Gesendet: Donnerstag, 17. September 2020 14:14
An: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] Prescan normalize and freesurfer


External Email - Use Caution
What head coil did you use?  Do you have a highres T2w or FLAIR?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Mikolas, Pavol" 
mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 17, 2020 at 7:12 AM
To: "'freesurfer@nmr.mgh.harvard.edu'" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution
Dear Freesurfer Developers,

I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using 
Freesurfer. I found out, that most of the scans were performed with the 
‘prescan normalize’ option. However, by approx..  12 % of participants, this 
option is missing. I also have complete data of all participants WITHOUT 
prescan normalize. In this analysis, we are interested in the correlation of GM 
volume in specific ROIs with clinical symptoms. Now we have two options:


  1.  Use the ‘prescan normalize’ dataset and account for the 12% without this 
option as a covariate
  2.  Use the complete dataset without ‘prescan normalize’

It would be very helpful, if you could share your arguments / experience with 
this, so that we proceed in the best manner.

Thank you, best regards

Pavol




The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


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intend

Re: [Freesurfer] Prescan normalize and freesurfer

[Glasser, Matthew]

External Email - Use Caution

Right I would recommend pre-scan normalize on for all images being acquired in 
a study.  There are important considerations for fMRI, diffusion, and ASL (and 
even auxiliary scans like SE fieldmaps) not just T1w/T2w/FLAIR.  That said, I 
was guessing that the FreeSurfer’s built in normalization could handle a 12CH 
receive field (based on my distant recollection of them) better than a 32CH 
receive field.

Matt.

From:  on behalf of "Fischl, Bruce" 

Reply-To: Freesurfer support list 
Date: Thursday, September 17, 2020 at 9:39 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Prescan normalize and freesurfer


I would guess it is pretty important for a 12 channel also, although it depends 
on field strength and also needs a body coil transmit to be maximally 
effective. In general we use it whenever we can

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Glasser, Matthew
Sent: Thursday, September 17, 2020 10:15 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Prescan normalize and freesurfer


External Email - Use Caution
Maybe Bruce or Doug wants to comment but probably if you are using a 12CH coil 
it isn’t so important to have on.  It’s pretty much required for a 32CH coil, 
as the bias field is quite fast.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Mikolas, Pavol" 
mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 17, 2020 at 9:02 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Prescan normalize and freesurfer



External Email - Use Caution
Dear Matthew,

thank you for this important point. I will check this. There might be just a 
few subjects with 8 and 32 head coil, so that it should be possible to discard 
them without affecting the sample size too much.

Do you think, you could give use some general hint to the ‘prescan normalize’ 
option? We cannot guess the benefit for our analysis well. Generally, if the 
benefit is rather low, we would tend to use the data without ‘prescan 
normalize’. What do you think?

Thank you, all best

Pavol


Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 Im Auftrag von Glasser, Matthew
Gesendet: Donnerstag, 17. September 2020 15:44
An: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] Prescan normalize and freesurfer


External Email - Use Caution
That alone will be a huge factor in variable SNR (and receive field).  Head 
coils are not interchangeable like that.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Mikolas, Pavol" 
mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 17, 2020 at 7:22 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution
Dear Matt,

unfortunately we have no highres T2w or FLAIR.
In this multicentric study, we tended to use the 12 head coil. However, some 
centers used a 8 or a 32 head coil.

Thanks

Pavol


Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 Im Auftrag von Glasser, Matthew
Gesendet: Donnerstag, 17. September 2020 14:14
An: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] Prescan normalize and freesurfer


External Email - Use Caution
What head coil did you use?  Do you have a highres T2w or FLAIR?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Mikolas, Pavol" 
mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 17, 2020 at 7:12 AM
To: "'freesurfer@nmr.mgh.harvard.edu'" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution
Dear Freesurfer Developers,

I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using 
Freesurfer. I found out, that most of the scans were performed with the 
‘prescan normalize’ option. However, by approx..  12 % of participants, this 
option is missing. I also have complete data of all participants WITHOUT 
prescan normalize. In this analysis, we are interested in the correlation of GM 
volume in specific ROIs with clinical symptoms. Now we have two options:


  1.  Use the ‘prescan normalize’

Re: [Freesurfer] arguments to use after pial edits {Disarmed}

[Glasser, Matthew]

External Email - Use Caution

I find the recon-all table to be helpful:

http://secure-web.cisco.com/1rQT1vL5GWrATp5z0Ct2LBj8MsEx75qijDiNOIOc1xsGTqc0VC-s7rH5tRIiUV_kHXR7CsV_-uoWR6y_oPuNxiCAZCmbkgfSfUxHd4oB4gX7XvLCt40MlQR_Ejq0tpN0lnJJt1uO1jl_1XWYZQv92-3NGME0PKZPC51_qjOKHk9cLfcojjN-AssGWAZ7y0t-UJXooxg2G2tzrQqm9emqIASj8_asI8t84TuQRjHEjkEj7KDq8IvfbXNQIT5xDLxB5A7a-aT2IrgX3QZs0Stdt7Q/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllTableStableV6.0

In this case, you probably need to run -autorecon2, as all subsequent steps are 
affected by the brainmask.mgz file.

Matt.

From:  on behalf of Darko Komnenić 

Reply-To: Freesurfer support list 
Date: Monday, November 30, 2020 at 12:49 PM
To: freesurfer 
Subject: [Freesurfer] arguments to use after pial edits {Disarmed}

External Email - Use Caution
Dear Freesurfer experts,
I am using Human Connectone Project pipelines to calculate cortical myelin 
levels. These pipelines use Freesurfer 6.
Since certain subjects' brain surfaces had some chunks and spikes sticking out, 
I edited the brainmask.mgz file for those subjects as described in this 
tutorial. MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1axQ4MDEpKp0YzmdtIT0FMnRvWx1u9q40rw_YBR1jd7UPMO5yuOexHcazdEVWBSweK7UbCLtoiXKiFhO5sdcYpFEOp2VdDUFETbARa89XLRDpy-On0Ag_IIBitDMwt5q2MvXdk-jXO64bglfH0cPWe3yJbcs0GiPGrKYuEVfUU6aPX19DRsci13lJU2XynUY_iYwvAzoTLgeXohO1QRDkJfiS1bUdZlelqV4Dr1VShu7obJEuTrdgrSpdZNbADK5KLHqSRHaOyz5PeoDLl0ND2g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FPialEdits_freeview

To get the myelin maps again, I got the instruction from the HCP mailing list 
that I should call again the FreeSurferPipeline script, but add the 
--existing-subject and --extra-reconall-arg flags.
If I understood correctly, after --extra-reconall-arg flag, there should be an 
equal sign, and then keywords that specify which recon-all stages I want to run.

Could you please tell me what those stages are, i.e. what keywords I should use 
after the equal sign? I want to keep the brainmask.mgz file that I edited, and 
then repeat all the steps that happen after braimask.mgz is generated. I was 
referred to the FS tutorials/wiki at the HCP mailing list, but I would like to 
double-check with someone here. Based on the tutorial link above, it seems this 
should be "-autorecon-pial -subjid pial_edits_before", but I'm not sure if this 
would be applicable in this case.

Thanks in advance and I hope my question wasn't too confusing.
Best,
Darko



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Re: [Freesurfer] arguments to use after pial edits

[Glasser, Matthew]

External Email - Use Caution

I think so.

Matt.

From:  on behalf of Darko Komnenić 

Reply-To: Freesurfer support list 
Date: Monday, November 30, 2020 at 6:23 PM
To: freesurfer 
Subject: Re: [Freesurfer] arguments to use after pial edits

External Email - Use Caution
Thanks Matt!
Should I also add the -autorecon3 flag, or does that get performed 
automatically if I put in "autorecon2"?
Best,
Darko


Message: 4
Date: Mon, 30 Nov 2020 19:16:06 +0000
From: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Subject: Re: [Freesurfer] arguments to use after pial edits {Disarmed}
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: 
<274fd511-f94f-4bc1-ae0c-804f1a6a3...@wustl.edu<mailto:274fd511-f94f-4bc1-ae0c-804f1a6a3...@wustl.edu>>
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

I find the recon-all table to be helpful:

http://secure-web.cisco.com/1rQT1vL5GWrATp5z0Ct2LBj8MsEx75qijDiNOIOc1xsGTqc0VC-s7rH5tRIiUV_kHXR7CsV_-uoWR6y_oPuNxiCAZCmbkgfSfUxHd4oB4gX7XvLCt40MlQR_Ejq0tpN0lnJJt1uO1jl_1XWYZQv92-3NGME0PKZPC51_qjOKHk9cLfcojjN-AssGWAZ7y0t-UJXooxg2G2tzrQqm9emqIASj8_asI8t84TuQRjHEjkEj7KDq8IvfbXNQIT5xDLxB5A7a-aT2IrgX3QZs0Stdt7Q/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllTableStableV6.0

In this case, you probably need to run -autorecon2, as all subsequent steps are 
affected by the brainmask.mgz file.

Matt.



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Re: [Freesurfer] Correcting pial surface with Flair sequence

[Glasser, Matthew]

External Email - Use Caution

You definitely want 3D sequences for FreeSurfer.  These can be T1w, T2w, or 
FLAIR.

Matt.

From:  on behalf of Georgia Kapizioni 

Reply-To: Freesurfer support list 
Date: Tuesday, January 5, 2021 at 5:37 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Correcting pial surface with Flair sequence



External Email - Use Caution
Hello Freesurfer Developers,

I am conducting a group analysis between a patients and a control group. I have 
accomplished recon-all individual analysis and I want to correct pial surface 
using 3D Flair.
I would like to ask two specific things:

1. Is 3D Flair appropriate or only T2 Flair is recommended for such correction. 
From what I have read on previous posts, it is usually recommended to use T2 
Flair.
2. For my data, for most of my 3D data slice thickness is 1 mm, but for some of 
them is 1.48 mm. Is that difference going to affect analysis results?


Thank you in advance,
Georgia


The materials in this message are private and may contain Protected Healthcare 
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intended recipient, be advised that any unauthorized use, disclosure, copying 
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Re: [Freesurfer] Correcting pial surface with Flair sequence

[Glasser, Matthew]

External Email - Use Caution

Since I don’t know what you are talking about, how about posting an image from 
the sequence you have in mind to use…

Matt.

From:  on behalf of Georgia Kapizioni 

Reply-To: Freesurfer support list 
Date: Thursday, January 7, 2021 at 11:05 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Correcting pial surface with Flair sequence



External Email - Use Caution
Thank you for your reply.

However, my questions referred to whether a 3D Flair could also work for pial 
surface correction, or only 3D T2 flair is suitable and if it is ok for all 
participants not to have the same slice thickness on Flair, as I previously 
wrote most of my participants have slice thickness 1mm but some have 1.48 mm.

Thanks again,
Georgia


On 6 Jan 2021, at 1:37 AM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Hello Freesurfer Developers,

I am conducting a group analysis between a patients and a control group. I have 
accomplished recon-all individual analysis and I want to correct pial surface 
using 3D Flair.
I would like to ask two specific things:

1. Is 3D Flair appropriate or only T2 Flair is recommended for such correction. 
From what I have read on previous posts, it is usually recommended to use T2 
Flair.
2. For my data, for most of my 3D data slice thickness is 1 mm, but for some of 
them is 1.48 mm. Is that difference going to affect analysis results?


Thank you in advance,
Georgia



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Re: [Freesurfer] Correcting pial surface with Flair sequence

[Glasser, Matthew]

External Email - Use Caution

You can always give it a try and put slice thickness as a covariate of no 
interest.

Matt.

From:  on behalf of Georgia Kapizioni 

Reply-To: Freesurfer support list 
Date: Friday, January 8, 2021 at 10:22 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Correcting pial surface with Flair sequence



External Email - Use Caution
Let me rephrase:

I am running an analysis with two groups, a patient group (n=23) and a healthy 
control group (n=24). I have accomplished 3DT1 recons for all participants. Now 
I want to correct pial surface using 3D Flair images.
However, I have different slice thickness among my participants’ flair images. 
Specifically for the patients’ group: 14 participants have slice thickness 1 mm 
but 9 have slice thickness 1.48mm (number of slices 209 for all participants) 
and in the control group I have for only 6 participants slice thickness 1 mm 
and for the rest 18 participants slice thickness 1.48  mm (again number of 
slices 209 for all participants).


Could someone please advice me whether I can use these Flair images to correct 
pial surface despite this slice thickness difference or is this difference 
going to be tricky for the results?


Thank you in advance,
Georgia


On 7 Jan 2021, at 7:05 PM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Thank you for your reply.

However, my questions referred to whether a 3D Flair could also work for pial 
surface correction, or only 3D T2 flair is suitable and if it is ok for all 
participants not to have the same slice thickness on Flair, as I previously 
wrote most of my participants have slice thickness 1mm but some have 1.48 mm.

Thanks again,
Georgia


On 6 Jan 2021, at 1:37 AM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Hello Freesurfer Developers,

I am conducting a group analysis between a patients and a control group. I have 
accomplished recon-all individual analysis and I want to correct pial surface 
using 3D Flair.
I would like to ask two specific things:

1. Is 3D Flair appropriate or only T2 Flair is recommended for such correction. 
From what I have read on previous posts, it is usually recommended to use T2 
Flair.
2. For my data, for most of my 3D data slice thickness is 1 mm, but for some of 
them is 1.48 mm. Is that difference going to affect analysis results?


Thank you in advance,
Georgia




The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
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Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Glasser, Matthew]

External Email - Use Caution

What scans are these?  I wasn’t aware of any 0.5mm scans.

Matt.

From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Thursday, January 21, 2021 at 12:21 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1





External Email - Use Caution
Hi there

As a follow-up to this question, I tried the flags as stated and the recon-all 
seems to have failed at the inflation stage:

/data-01/trisanna/freesurfer/freesurfer_7.1.1/TEST2/scripts

 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix 
../surf/lh.qsphere.nofix

doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
version: 7.1.1
available threads: 1
scaling brain by 0.274...
inflating...
Command terminated by signal 11
@#@FSTIME  2021:01:21:08:13:01 mris_sphere N 9 e 4.07 S 0.18 U 3.72 P 95% M 
281092 F 17 R 136514 W 0 c 337 w 22 I 4312 O 0 L 1.00 1.00 1.00
@#@FSLOADPOST 2021:01:21:08:13:06 mris_sphere N 9 1.00 1.00 1.00
Linux kaplan 4.15.0-132-generic #136~16.04.1-Ubuntu SMP Tue Jan 12 18:22:20 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s TEST2 exited with ERRORS at Thu Jan 21 08:13:06 EST 2021



Any advice would be greatly appreciated,

Trisanna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Trisanna Sprung-Much 

Sent: Tuesday, January 19, 2021 6:05 PM
To: Freesurfer support list 
Subject: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution
Hi there

If I want to run some HCP subjects that are 0.5mm iso T1w scans (MPRAGE) in 
FreeSurfer 7.1, would I simply use the following flags, or am I missing 
something?

 -3T -MPRAGE -hires

Do we need an expert file with version 7.1 to specify the number of iterations 
for surface inflation or is this now done automatically?

Thank you
Trisanna


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
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Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Glasser, Matthew]

External Email - Use Caution

You are likely to get significantly worse results by reprocessing the HCP 
subjects with FreeSurfer 7.X.  Unfortunately it has issues with HCP data that 
haven’t been addressed yet.

Matt.

From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 9:13 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1





External Email - Use Caution
Hi Doug and Matt

So the HCP scans are at 0.5mm resolution because they were originally 0.7mm and 
have been registered to our 0.5mm MNI152 template, to avoid losing data by 
registering to the 1mm template. That's all.

As for the recon-all.log, unfortunately I deleted it when I re-ran the same 
subject this weekend using an -expert file to specify the number of inflations 
and it worked. It took 24 hrs.

I will try to run another subject without the expert file, since Doug says this 
should not be necessary, and get back to you ASAP.

Best
Trisanna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Monday, January 25, 2021 11:22 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

You don't need any special flags with the -hires option. Also, it is helpful to 
include the recon-all.log file.
On 1/22/2021 12:15 AM, Glasser, Matthew wrote:

External Email - Use Caution

What scans are these?  I wasn’t aware of any 0.5mm scans.



Matt.



From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, January 21, 2021 at 12:21 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1





External Email - Use Caution

Hi there



As a follow-up to this question, I tried the flags as stated and the recon-all 
seems to have failed at the inflation stage:



/data-01/trisanna/freesurfer/freesurfer_7.1.1/TEST2/scripts



 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix 
../surf/lh.qsphere.nofix



doing quick spherical unfolding.

limitting unfolding to 6 passes

using n_averages = 128

setting seed for random number genererator to 1234

version: 7.1.1

available threads: 1

scaling brain by 0.274...

inflating...

Command terminated by signal 11

@#@FSTIME  2021:01:21:08:13:01 mris_sphere N 9 e 4.07 S 0.18 U 3.72 P 95% M 
281092 F 17 R 136514 W 0 c 337 w 22 I 4312 O 0 L 1.00 1.00 1.00

@#@FSLOADPOST 2021:01:21:08:13:06 mris_sphere N 9 1.00 1.00 1.00

Linux kaplan 4.15.0-132-generic #136~16.04.1-Ubuntu SMP Tue Jan 12 18:22:20 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux



recon-all -s TEST2 exited with ERRORS at Thu Jan 21 08:13:06 EST 2021







Any advice would be greatly appreciated,



Trisanna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Sent: Tuesday, January 19, 2021 6:05 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] HCP T1w scans on FreeSurfer 7.1



External Email - Use Caution

Hi there



If I want to run some HCP subjects that are 0.5mm iso T1w scans (MPRAGE) in 
FreeSurfer 7.1, would I simply use the following flags, or am I missing 
something?



 -3T -MPRAGE -hires



Do we need an expert file with version 7.1 to specify the number of iterations 
for surface inflation or is this now done automatically?



Thank you

Trisanna





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.



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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
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Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Glasser, Matthew]

External Email - Use Caution

That’s not a good idea either.

Matt.

From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 9:30 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

Why are you registering it to the MNI prior to FS analysis?
On 1/26/2021 10:13 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution
Hi Doug and Matt

So the HCP scans are at 0.5mm resolution because they were originally 0.7mm and 
have been registered to our 0.5mm MNI152 template, to avoid losing data by 
registering to the 1mm template. That's all.

As for the recon-all.log, unfortunately I deleted it when I re-ran the same 
subject this weekend using an -expert file to specify the number of inflations 
and it worked. It took 24 hrs.

I will try to run another subject without the expert file, since Doug says this 
should not be necessary, and get back to you ASAP.

Best
Trisanna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Monday, January 25, 2021 11:22 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

You don't need any special flags with the -hires option. Also, it is helpful to 
include the recon-all.log file.
On 1/22/2021 12:15 AM, Glasser, Matthew wrote:

External Email - Use Caution

What scans are these?  I wasn’t aware of any 0.5mm scans.



Matt.



From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, January 21, 2021 at 12:21 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1





External Email - Use Caution

Hi there



As a follow-up to this question, I tried the flags as stated and the recon-all 
seems to have failed at the inflation stage:



/data-01/trisanna/freesurfer/freesurfer_7.1.1/TEST2/scripts



 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix 
../surf/lh.qsphere.nofix



doing quick spherical unfolding.

limitting unfolding to 6 passes

using n_averages = 128

setting seed for random number genererator to 1234

version: 7.1.1

available threads: 1

scaling brain by 0.274...

inflating...

Command terminated by signal 11

@#@FSTIME  2021:01:21:08:13:01 mris_sphere N 9 e 4.07 S 0.18 U 3.72 P 95% M 
281092 F 17 R 136514 W 0 c 337 w 22 I 4312 O 0 L 1.00 1.00 1.00

@#@FSLOADPOST 2021:01:21:08:13:06 mris_sphere N 9 1.00 1.00 1.00

Linux kaplan 4.15.0-132-generic #136~16.04.1-Ubuntu SMP Tue Jan 12 18:22:20 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux



recon-all -s TEST2 exited with ERRORS at Thu Jan 21 08:13:06 EST 2021







Any advice would be greatly appreciated,



Trisanna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Sent: Tuesday, January 19, 2021 6:05 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] HCP T1w scans on FreeSurfer 7.1



External Email - Use Caution

Hi there



If I want to run some HCP subjects that are 0.5mm iso T1w scans (MPRAGE) in 
FreeSurfer 7.1, would I simply use the following flags, or am I missing 
something?



 -3T -MPRAGE -hires



Do we need an expert file with version 7.1 to specify the number of iterations 
for surface inflation or is this now done automatically?



Thank you

Trisanna





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.



___

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Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Glasser, Matthew]

External Email - Use Caution

Please explain what you are doing that requires this.  There are many good 
reasons why this is not the approach FreeSurfer or the HCP have taken.  Not the 
least of which is that all volumetrics and morphometrics will be invalid if not 
measured in the subject’s own physical space.

Matt.

From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 9:53 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1





External Email - Use Caution
Hi Matt

We want the surfaces to be extracted from volumes that have been registered to 
MNI152, rather than extracting the surfaces in the native space of the subject, 
which is what FreeSurfer does.

I have done this for 2 other projects in the past for ICBM data (not HCP) and 
it worked fine.

What would be the concern with the HCP data?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Glasser, Matthew 

Sent: Tuesday, January 26, 2021 11:45 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution

That’s not a good idea either.



Matt.



From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 9:30 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1



Why are you registering it to the MNI prior to FS analysis?

On 1/26/2021 10:13 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

Hi Doug and Matt



So the HCP scans are at 0.5mm resolution because they were originally 0.7mm and 
have been registered to our 0.5mm MNI152 template, to avoid losing data by 
registering to the 1mm template. That's all.



As for the recon-all.log, unfortunately I deleted it when I re-ran the same 
subject this weekend using an -expert file to specify the number of inflations 
and it worked. It took 24 hrs.



I will try to run another subject without the expert file, since Doug says this 
should not be necessary, and get back to you ASAP.



Best

Trisanna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Monday, January 25, 2021 11:22 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1



You don't need any special flags with the -hires option. Also, it is helpful to 
include the recon-all.log file.

On 1/22/2021 12:15 AM, Glasser, Matthew wrote:

External Email - Use Caution

What scans are these?  I wasn’t aware of any 0.5mm scans.



Matt.



From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, January 21, 2021 at 12:21 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1





External Email - Use Caution

Hi there



As a follow-up to this question, I tried the flags as stated and the recon-all 
seems to have failed at the inflation stage:



/data-01/trisanna/freesurfer/freesurfer_7.1.1/TEST2/scripts



 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix 
../surf/lh.qsphere.nofix



doing quick spherical unfolding.

limitting unfolding to 6 passes

using n_averages = 128

setting seed for random number genererator to 1234

version: 7.1.1

available threads: 1

scaling brain by 0.274...

inflating...

Command terminated by signal 11

@#@FSTIME  2021:01:21:08:13:01 mris_sphere N 9 e 4.07 S 0.18 U 3.72 P 95% M 
281092 F 17 R 136514 W 0 c 337 w 22 I 4312 O 0 L 1.00 1.00 1.00

@#@FSLOADPOST 2021:01:21:08:13:06 mris_sphere N 9 1.00 1.00 1.00

Linux kaplan 4.15.0-132-generic #136~16.04.1-Ubuntu SMP Tue Jan 12 18:22:20 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux



recon-all -s TEST2 exited with ERRORS at Thu Jan 21 08:13:06 EST 2021







Any advice would be greatly appreciated,



Trisanna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Sent: Tuesday, January 19, 2021 6:05 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] HCP T1w scans on FreeSurfer 7.1



External Email - Use Caution

Hi there



If I want to run some HCP subjects that are 0.5mm iso T1w sc

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Glasser, Matthew]

External Email - Use Caution

I think it would be a good idea to take a step back and tell us what you are 
trying to accomplish.  This is all not the right way to go about things.  The 
HCP already produces surfaces registered to MNI space in the volume for example.

Matt.

From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 9:45 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

* External Email - Caution *

External Email - Use Caution
Hi Matt

The sole purpose of using 7.1 is to be able to create labels directly on the 
surfaces (painting sulci). For the 1 subject that I ran successfully  - the 
surfaces are decent, although a bit bumpy, perhaps because it is -hires. See 
images attached.

I will test another few subjects today and get back to this email.

Best,
Trisanna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Glasser, Matthew 

Sent: Tuesday, January 26, 2021 11:28 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution

You are likely to get significantly worse results by reprocessing the HCP 
subjects with FreeSurfer 7.X.  Unfortunately it has issues with HCP data that 
haven’t been addressed yet.



Matt.



From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 9:13 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1





External Email - Use Caution

Hi Doug and Matt



So the HCP scans are at 0.5mm resolution because they were originally 0.7mm and 
have been registered to our 0.5mm MNI152 template, to avoid losing data by 
registering to the 1mm template. That's all.



As for the recon-all.log, unfortunately I deleted it when I re-ran the same 
subject this weekend using an -expert file to specify the number of inflations 
and it worked. It took 24 hrs.



I will try to run another subject without the expert file, since Doug says this 
should not be necessary, and get back to you ASAP.



Best

Trisanna



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Monday, January 25, 2021 11:22 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1



You don't need any special flags with the -hires option. Also, it is helpful to 
include the recon-all.log file.

On 1/22/2021 12:15 AM, Glasser, Matthew wrote:

External Email - Use Caution

What scans are these?  I wasn’t aware of any 0.5mm scans.



Matt.



From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, January 21, 2021 at 12:21 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1





External Email - Use Caution

Hi there



As a follow-up to this question, I tried the flags as stated and the recon-all 
seems to have failed at the inflation stage:



/data-01/trisanna/freesurfer/freesurfer_7.1.1/TEST2/scripts



 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix 
../surf/lh.qsphere.nofix



doing quick spherical unfolding.

limitting unfolding to 6 passes

using n_averages = 128

setting seed for random number genererator to 1234

version: 7.1.1

available threads: 1

scaling brain by 0.274...

inflating...

Command terminated by signal 11

@#@FSTIME  2021:01:21:08:13:01 mris_sphere N 9 e 4.07 S 0.18 U 3.72 P 95% M 
281092 F 17 R 136514 W 0 c 337 w 22 I 4312 O 0 L 1.00 1.00 1.00

@#@FSLOADPOST 2021:01:21:08:13:06 mris_sphere N 9 1.00 1.00 1.00

Linux kaplan 4.15.0-132-generic #136~16.04.1-Ubuntu SMP Tue Jan 12 18:22:20 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux



recon-all -s TEST2 exited with ERRORS at Thu Jan 21 08:13:06 EST 2021







Any advice would be greatly appreciated,



Trisanna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Sent: Tuesday, January 19, 2021 6:05 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] HCP T1w scans on FreeSurfer 7.1



External Email - Use Caution

Hi there



If I want to run some HCP subjects that are 0.5mm iso T1w scans (MPRAGE) in 
FreeSurfer 7.1, would I simply use the following flags, or am I missing 
something?



 -3T -MPRAGE -hires



Do we need an expert file with version 7.1 to specify the number of iterations 
for surface

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Glasser, Matthew]

External Email - Use Caution

Right just use the surfaces in ${StudyFolder}/${Subject}/MNINonLinear.  These 
are in MNI space and should work for you.  They are in GIFTI format, which is 
readable by FreeView.

In the future, it is trivial to move surfaces to MNI space after they were 
computed in subject’s physical space with Connectome Workbench and FreeSurfer 
probably has tools for this as well.

Matt.

From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 12:24 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution
Hi Bruce

Thanks for your speedy response. This would be an immense time saver if this 
works. I will give this a go.
Yes, you are correct about the blurring as well!

Best

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of "Fischl, Bruce" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 1:22 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

Hi Trisanna

Yes, I’m pretty sure that would work. That is, using the current freeview on 
older versions of recon data.

Cheers
Bruce

p.s. one addendum – you should not have to blur the labels after registration, 
assuming your manually labeled dataset is big enough

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trisanna Sprung-Much
Sent: Tuesday, January 26, 2021 1:13 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution
Hi Matt

OK, I think there has been some confusion and I think I just realized what it 
is. I am from the MNI and we are used to using the ICBM database, not HCP 
database. We are also used to painting sulci in volumetric form, so we always 
used to register our scans to MNI space (linear) prior to painting. We never 
computed any volumetric/morphometric data of the scans, so we went ahead with 
this registration to MNI space simply for painting in a common space.

What we now wish to do this year is:
Paint individual sulci directly on subject surfaces
Register the labels to fsaverage
Average and blur the labels to generate surface probability maps on fsaverage

We went the route of looking at Freesurer 7.1 because one can paint directly on 
surfaces in Freeview. I therefore did not at all use the HCP pipeline but 
simply tested recon-all on HCP volumes using Freesufer 7.1. We can of course 
use the native scans instead of those registered to MNI152 space.

My question is the following: Could one simply use the HCP pipeline output from 
the Human Connectome, convert the surfaces so they can be loaded into Freeview 
7.1, and paint directly on these? This would save us from having to re-run all 
HCP subjects with recon-all in 7.1….

Best,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Glasser, Matthew" mailto:glass...@wustl.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, January 26, 2021 at 11:01 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution
I think it would be a good idea to take a step back and tell us what you are 
trying to accomplish.  This is all not the right way to go about things.  The 
HCP already produces surfaces registered to MNI space in the volume for example.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Trisanna Sprung-Much 
mailto:trisanna.sprung-m...@mail.mcgill.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, January 26, 2021 at 9:45 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

* External Email - Caution *

External Email - Use Caution
Hi Matt

The sole purpose of using 7.1 is to be able to create labels directly on the 
surfaces (painting sulci). For the 1 subject that I ran successfully  - the 
surfaces are decent, although a bit bumpy, perhaps because it is -hires. See 
images attached.

I will test another few subjects today and get back to this email.

Best,
Trisanna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Tuesday, January 26, 2021 11:28 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution

You are lik

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Glasser, Matthew]

External Email - Use Caution

Sorry I’m completely confused now about what you are trying to do.  The data in 
${StudyFolder}/${Subject}/T1w is also in MNI space, but after only a 6 DOF 
rigid registration (i.e. no changes in brain shape, just a similar brain 
orientation and AC at 0,0,0).  What does “paint surfaces” mean anyhow?

Matt.

From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 1:00 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution
Thanks for this Matt.
Just a question – is it called “MNINonlinear” because a non-linear registration 
was used to MNIspace? If this is the case, I would prefer to paint in the 
subject’s native space.

Best,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 1:57 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution
Right just use the surfaces in ${StudyFolder}/${Subject}/MNINonLinear.  These 
are in MNI space and should work for you.  They are in GIFTI format, which is 
readable by FreeView.

In the future, it is trivial to move surfaces to MNI space after they were 
computed in subject’s physical space with Connectome Workbench and FreeSurfer 
probably has tools for this as well.

Matt.

From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 12:24 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution
Hi Bruce

Thanks for your speedy response. This would be an immense time saver if this 
works. I will give this a go.
Yes, you are correct about the blurring as well!

Best

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of "Fischl, Bruce" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 1:22 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

Hi Trisanna

Yes, I’m pretty sure that would work. That is, using the current freeview on 
older versions of recon data.

Cheers
Bruce

p.s. one addendum – you should not have to blur the labels after registration, 
assuming your manually labeled dataset is big enough

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trisanna Sprung-Much
Sent: Tuesday, January 26, 2021 1:13 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution
Hi Matt

OK, I think there has been some confusion and I think I just realized what it 
is. I am from the MNI and we are used to using the ICBM database, not HCP 
database. We are also used to painting sulci in volumetric form, so we always 
used to register our scans to MNI space (linear) prior to painting. We never 
computed any volumetric/morphometric data of the scans, so we went ahead with 
this registration to MNI space simply for painting in a common space.

What we now wish to do this year is:
Paint individual sulci directly on subject surfaces
Register the labels to fsaverage
Average and blur the labels to generate surface probability maps on fsaverage

We went the route of looking at Freesurer 7.1 because one can paint directly on 
surfaces in Freeview. I therefore did not at all use the HCP pipeline but 
simply tested recon-all on HCP volumes using Freesufer 7.1. We can of course 
use the native scans instead of those registered to MNI152 space.

My question is the following: Could one simply use the HCP pipeline output from 
the Human Connectome, convert the surfaces so they can be loaded into Freeview 
7.1, and paint directly on these? This would save us from having to re-run all 
HCP subjects with recon-all in 7.1….

Best,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Glasser, Matthew" mailto:glass...@wustl.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, January 26, 2021 at 11:01 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution
I think it would be a good idea to take a step back and tell us what you are 
trying to accomplish.  This is all not the right way to go about things.  The 
HCP already produces surfaces registered to MNI space in the volume for example.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Trisanna Sprung-Much 
mailto:trisanna.sprung-m...@mail.mcgill.ca>>
Reply-To: Freesurfer support list 
mailto:f

Re: [Freesurfer] Cortical thickness on version 6 vs 7

[Glasser, Matthew]

External Email - Use Caution

For what it’s worth, we had problems with FreeSurfer 7.X with surface placement 
accuracy on HCP-Style data (i.e. 0.8-0.7mm isotropic T1w and T2w) and have 
continued to recommend using FreeSurfer 6 for the HCP Pipelines for now.  We 
usually quote 2.6mm average cortical thickness for young adults, but it does 
depend on age.

Matt.

From:  on behalf of Xiaojiang Yang 

Reply-To: Freesurfer support list 
Date: Friday, March 12, 2021 at 10:29 AM
To: Freesurfer support list 
Subject: [Freesurfer] Cortical thickness on version 6 vs 7



External Email - Use Caution
Dear Freesurfer developers,

I have a cohort of subjects that are already run under FS 6. I recently 
upgraded Freesurfer from 6.0 to 7.1.1, and now I also have run these subjects 
under FS 7.

When comparing the cortical thickness results obtained from FS6 and FS7, I 
found that FS 7 results are much smaller than the FS6 ones. On average, about 
13%-21% decrease in the subject's average cortical thickness. Specifically, on 
a cohort of images from GE scanners, the average cortical thickness from FS6 is 
2.5mm, but from FS7 is less than 2.0mm.

According to some published papers, I think 2.5mm as the average cortical 
thickness is more accurate than 2.0mm.

Have you encountered this issue or question before? Do you think I should keep 
using FS6? Please give me your advice. Thank you!

John.



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Meylin overlay

[Glasser, Matthew]

External Email - Use Caution

You should be able to load files like 
${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.${Hemisphere}.MyelinMap[_BC].native.func.gii
 in Freeview.

Matt.

From:  on behalf of バキット・ムダシル 

Reply-To: Freesurfer support list 
Date: Monday, March 15, 2021 at 10:18 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Meylin overlay



External Email - Use Caution
Dear freesurfer experts,

Is there a way to import the individual surface myelin maps from the human 
connectome project database to freesurfer and use them as overlays? Or can we 
create them in freesurfer?

Mudathir







The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Meylin overlay

[Glasser, Matthew]

External Email - Use Caution

There is a bug in Freeview, I believe it has been fixed in the dev build.

Matt.

From:  on behalf of バキット・ムダシル 

Reply-To: Freesurfer support list 
Date: Tuesday, March 16, 2021 at 10:38 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Meylin overlay



External Email - Use Caution
Thanks Matt. I tried it with version 7.1.1 of freesurfer didn’t work but worked 
fine with freesurfer 6. With version 7.1 it failed to load the gii file. Any 
idea how to fix it?

Mudathir





On Mar 16, 2021, at 21:08, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

External Email - Use Caution

You should be able to load files like 
${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.${Hemisphere}.MyelinMap[_BC].native.func.gii
 in Freeview.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of バキット・ムダシル mailto:m-bak...@fmu.ac.jp>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, March 15, 2021 at 10:18 PM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Meylin overlay

External Email - Use Caution
Dear freesurfer experts,

Is there a way to import the individual surface myelin maps from the human 
connectome project database to freesurfer and use them as overlays? Or can we 
create them in freesurfer?

Mudathir








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Re: [Freesurfer] equivolumetric surfaces

[Glasser, Matthew]

External Email - Use Caution

You can do this with Connectome Workbench command (wb_command -surface-layer 
and wb_command -volume-to-surface-mapping).

Matt.

From:  on behalf of バキット・ムダシル 

Reply-To: Freesurfer support list 
Date: Friday, March 19, 2021 at 2:21 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] equivolumetric surfaces

External Email - Use Caution
Dear freesurfer experts,

I want to create an equivolumetric surfaces (using the tool from: MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://github.com/kwagstyl/surface_tools)
 and to sample the intensities of the T1wDividedByT2w volume at all the depths. 
I created the surfaces and after running the mri_vol2surf command I faced the 
error below. I don’t know why the path to the surface is not correct. I tried 
it in different devices with different versions of freesurfer but the results 
were the same. Any idea what I did wrong? Thanks

Mudathir

#
 freesurfer-darwin-macOS-7.1.1-20200811-8b40551 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.1.1
FSFAST_HOME   /Applications/freesurfer/7.1.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.1.1/subjects
MNI_DIR   /Applications/freesurfer/7.1.1/mni
FSL_DIR   /usr/local/fsl
mudathir% mri_vol2surf --src $SUBJECTS_DIR/spl_01/mri/T1wDividedByT2w.nii.gz 
--out $SUBJECTS_DIR/spl_01/lh.equi_intensity_1.0.mgh --hemi lh --surf 
$SUBJECTS_DIR/spl_01/surf/lh.equi1.0.pial --out_type mgh --regheader spl_01
srcvol = 
/Applications/freesurfer/7.1.1/subjects/spl_01/mri/T1wDividedByT2w.nii.gz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /Applications/freesurfer/7.1.1/subjects/spl_01/mri/orig.mgz as target 
reference.
 original matrix ---
 1.0   0.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0  -1.0   0.0   0.35001;
 0.0   0.0   0.0   1.0;
 original matrix ---
Reading surface 
/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
error: No such file or directory
error: 
MRISread(/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial):
 could not open file
error: No such file or directory
error: mri_vol2surf: could not read surface 
/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
mudathirbakhit%
#




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Re: [Freesurfer] Export stats: HCP Multi Modal parcellation

[Glasser, Matthew]

External Email - Use Caution

What stats are you looking for?

Matt.

From:  on behalf of Miguel Ángel Rivas 
Fernández 
Reply-To: Freesurfer support list 
Date: Wednesday, March 31, 2021 at 4:36 AM
To: Freesurfer support list 
Subject: [Freesurfer] Export stats: HCP Multi Modal parcellation



External Email - Use Caution

Dear Freesurfer experts,

it is possible to export the stats of subjects reconstructed with freesurfer 
v.6 using the HCP Multi Modal parcellation? (Glasser et al., 2016).

Thank you in advance.

Best regards,

--
Miguel Ángel Rivas Fernández



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Re: [Freesurfer] Export stats: HCP Multi Modal parcellation

[Glasser, Matthew]

External Email - Use Caution

It might be necessary to resample the atlas to the native mesh surfaces and 
convert it to the .annot file format from GIFTI.  The former can be done using 
these instructions to get to fsaverage and then presumably FreeSurfer has a 
tool to get it to the native mesh and the latter with mris_convert:

https://secure-web.cisco.com/14YUuLKxR8nqmyOxrwK7DZrs4RQGGbNtr7w49dQj1Ij4Zka4d4kqMQf275lQEk6s5VCtrGZPFMLxTlGUIqPf4V-tscwWLIQzYWUvmfU3jwE7Xv0thgSwKkkmAfDxfjkDsw6P0Hr1NZNA98__f-Fq5ofMbHzIllAPPFaqe2oNp8paK-232vTFTzsCdsZhFbHVvg4X_hHh_jzQEPzoJNzF9NmKPDTCcuER-vIOeOieDje8g6UVl4R8Rl-5lSe63qeZ9ZZKTII7lwJP9kq4e_3tYeg/https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP.pdf

Matt.

From:  on behalf of Miguel Ángel Rivas 
Fernández 
Reply-To: Freesurfer support list 
Date: Wednesday, March 31, 2021 at 8:58 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Export stats: HCP Multi Modal parcellation



External Email - Use Caution
Hello Glasser,

In addition to freesurfer's asegstats2table, I would be interested in volume, 
cortical thickness and area of the HCP atlas (please, see attached .csv file). 
Other software (e.g 
CAT12<http://secure-web.cisco.com/1COAdbRtDckHN6yiHBswwxyVsNqxiQs4J0BIS3hCQNJzehplVAuaKl0ugaaaCSeAfNzGdiJpsvU6rvCBU9qIhWpNEmuB5E_ojQBwSRyr9qaSyv5oU0ed91aiW7flrQXvoPLoIyDuKczkUZI6P9NtmVQQqy01bFfwg_qZ8BES-sVkfG4hnppkEYdZb_dXubwS-Xt-QLigkXU9P3ZcpEIZB1hUvLLXtw-RM99oapY7Dm8XYjdgD9PM7R654BuszY4iuqGBnbLgZEA4VGHPlQJsk9A/http%3A%2F%2Fwww.neuro.uni-jena.de%2Fcat12-html%2Fcat_methods_RBM.html%23FS_HCP>)
 allows exporting these measurements in HCP parcellation but I would like to 
know if it is possible with MRI data processed un FS.v6

Thank you in advance.


Best regards,
#

El mié., 31 mar. 2021 15:28, Glasser, Matthew 
mailto:glass...@wustl.edu>> escribió:

External Email - Use Caution
What stats are you looking for?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Miguel Ángel Rivas Fernández 
mailto:miguelrivasf...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, March 31, 2021 at 4:36 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Export stats: HCP Multi Modal parcellation



External Email - Use Caution

Dear Freesurfer experts,

it is possible to export the stats of subjects reconstructed with freesurfer 
v.6 using the HCP Multi Modal parcellation? (Glasser et al., 2016).

Thank you in advance.

Best regards,

--
Miguel Ángel Rivas Fernández



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Re: [Freesurfer] Native volume to fs_average surface

[Glasser, Matthew]

External Email - Use Caution

You would do that through the subject’s own surface.  It does not work very 
well to map data directly from the volume onto group average surfaces (see e.g. 
Coalson et al., 2018 PNAS).

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, April 19, 2021 at 4:23 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: [Freesurfer] Native volume to fs_average surface





External Email - Use Caution
Hi experts,

I have some fMRI data that I have pre-processed in Feat. I want to resample a 
single subject's data to the fs_average surface but unsure of the most optimal 
way of doing this. At present I am warping the functional data to the MNI brain 
in the volume (using FSL's applywarp) and then resampling to fs_average using 
the following command.

  *   mri_vol2surf --src filtered_func_MNI.nii --out filtered_func_surf.mgh 
--hemi rh --mni152reg

My question is whether you think this is the most appropriate approach, and/or 
if there is way to move directly from native volume to fs_average surface 
without needing to go via MNI volume?

Best wishes,
Mason


Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK



Email: wells...@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University 
webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU



E-bost: wells...@caerdydd.ac.uk

Ffôn: 02920 879628



The materials in this message are private and may contain Protected Healthcare 
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Re: [Freesurfer] Native volume to fs_average surface

[Glasser, Matthew]

External Email - Use Caution

What is most important is that you map to your individual’s surface (whether 
that is in subject’s physical space or MNI space doesn’t matter so much).  If 
you are using FreeSurfer formatted data, others can suggest how to do this.  
With NIFTI/GIFTI/CIFTI, it can be accomplished with wb_command 
-volume-to-surface-mapping and wb_command -metric-resampling among other things 
(e.g. see 
https://secure-web.cisco.com/1_Cq1etkFEJqfTFb_02eCv_lWyZdh6vGfkdd5A81SPw-162gbs9u3HNA1PnuI7IsLrhkGjH3RxADhe1uk6zpOS4uCtg9YOdXFh8Z0VVcD8z-PgaZzq3v-LlDwgk5DfFfrJE-OMomZ4ZIA9-Q8Ihk3gRZ0O4LWEOd6nvAZ3AdlWe0nxXANY2zKCNEgv_fUrnQq3PJEce8MeX5SdLB-FImrnAJX6gVvKh18gh6sVI9yzAfTF0TcJQ5eLy-JcnQzrOFcFPp4ssonrJT6Tcfqvk0m3w/https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Fblob%2Fmaster%2FfMRISurface%2Fscripts%2FRibbonVolumeToSurfaceMapping.sh).

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, April 19, 2021 at 4:45 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Native volume to fs_average surface





External Email - Use Caution
HI Matt,

Thanks for the reply. Are you suggesting I go native volume > native surface > 
fs_average? If so, can you recommend the best can I go from native to group 
average surface?


Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK



Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>

Tel: 02920 879628

Web: Cardiff University 
webpage<https://secure-web.cisco.com/1WCYtSJa5SHotGCjKhAFSbD5jLy8xDueFAXlo_Vfk4WyJYhmxG18wqrEdh7CeV9mTj0Yb7tToqiZMK4BjCFizdNLYH-N2qvjFZBXjjzVuk0nOXKbFz3rLcfLKc77KhBxYw2suMHL8dMUCIZ0vIMWlmuRmZs1uINijmQi7svdcv2YBL1R8vQUNfhn7rQ5pLqWHn2eWdo7IanPd1h6fPoMcy5VcpnSbVH67JcPU0KQ3mtscRkf1cHQvi9AI1FyOEDOUp5V2kArCuIYHZhmkJvixJg/https%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F974214->

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU



E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>

Ffôn: 02920 879628


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Glasser, Matthew 

Sent: Monday, April 19, 2021 10:27 AM
To: Freesurfer support list ; 
freesurfer-boun...@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Native volume to fs_average surface

External email to Cardiff University - Take care when replying/opening 
attachments or links.
Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor 
atodiadau neu ddolenni.


External Email - Use Caution

You would do that through the subject’s own surface.  It does not work very 
well to map data directly from the volume onto group average surfaces (see e.g. 
Coalson et al., 2018 PNAS).



Matt.



From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, April 19, 2021 at 4:23 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: [Freesurfer] Native volume to fs_average surface





External Email - Use Caution

Hi experts,



I have some fMRI data that I have pre-processed in Feat. I want to resample a 
single subject's data to the fs_average surface but unsure of the most optimal 
way of doing this. At present I am warping the functional data to the MNI brain 
in the volume (using FSL's applywarp) and then resampling to fs_average using 
the following command.

  *   mri_vol2surf --src filtered_func_MNI.nii --out filtered_func_surf.mgh 
--hemi rh --mni152reg



My question is whether you think this is the most appropriate approach, and/or 
if there is way to move directly from native volume to fs_average surface 
without needing to go via MNI volume?



Best wishes,

Mason



Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK



Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>

Tel: 02920 879628

Web: Cardiff University 
webpage<https://secure-web.cisco.com/18O020vXZIBYv3rUYS23vBvT7-YRSZBgjnRI_go1CHmqQMbwh6GID35oDZggTwSjB6Md_DuRp_nDCUkFRY-6c2orqtuwJGTRqttD3iAJ4pIxBGTRvzKvN59twE41VodR9ytmOrr8ZVoQgxtGpIGoB2e1LasEF77yrdUTjNkVv84efTHknXLMql-W6MvdXCr9W42YpIqL1DcqdjzCV5jaeDDDa4MLTajbtTMlzupt-homHrknIJgWnc7qIEv2AF0Rg-G8YD4WdmdCROidFeaWpdw/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1qGEoQnnU3besQKg-GQwdKq-WtCCzi1b5tl-HNLywYRQ48GHFhy2hNJxQfxY9t4vTe7V1-y5Gueo1-GHgls6xg6bCuHa7_Jm97SAxD4oOE1Uz

Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

[Glasser, Matthew]

External Email - Use Caution

One reason Bruce may be asking why you need MNI coordinates is that MNI 
coordinates are a very poor substitute for surface-based statistical maps and a 
terrible way to compare across subjects.  It’s much better to align subjects on 
the surface and then make much more accurate comparisons.  If you have volume 
coordinates from an individual subject, you can project those accurately onto 
that subject’s cortical surface.  In Connectome Workbench we do this with Foci, 
but I bet FreeSurfer has something similar.  You just need to ensure that the 
coordinates and the surface are in the same volume space (i.e. are aligned with 
eachother).  This could be in the subject’s physical space or MNI space (keep 
in mind that FreeSurfer never puts surfaces in MNI space, but we make copies of 
them there in the HCP Pipelines).

I also see you asked how to convert .mgh to a Connectome Workbench readable 
format.  I must admit I’m not entirely sure what .mgh contains.  If it is a 
value per vertex, you could likely use mris_convert to do the conversion to 
.func.gii.  .annot can be converted to .label.gii with mris_convert.

Matt.

From:  on behalf of "Fischl, Bruce" 

Reply-To: Freesurfer support list 
Date: Sunday, May 16, 2021 at 7:34 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas


Hi Sara

Why do you need MNI coordinates at all?

Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Romanella,Sara (BIDMC - 
Wilkinson - Neurology SF)
Sent: Sunday, May 16, 2021 5:57 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas


​Hi Bruce,

I can convert the MNI coordinates to subject space. But how do I enter them in 
freeview when I open the DK atlas of the subject to see where they fall?

thank you for the help!


Sara Romanella
Fellow (Ph.D. in Neuroscience)
Berenson-Allen Center for Noninvasive Brain Stimulation
Department of Neurology | Beth Israel Deaconess Medical Center
330 Brookline Avenue, 02215 Boston, MA, USA
Phone Nr: +1-339-229-7645

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>
Sent: Sunday, May 16, 2021 10:31 AM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Hi Sara

Why do you need MNI at all? Why not just do it in individual subject space?
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF)
Sent: Saturday, May 15, 2021 8:43 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas


​I am actually not sure. I have some MNI coordinates for the GM surface and I 
should check if they fall into a specific area of the DK. I could sacrifice 
accuracy in order to check this.

Could you please me tell me how if possible?

Thank you!


Sara Romanella
Fellow (Ph.D. in Neuroscience)
Berenson-Allen Center for Noninvasive Brain Stimulation
Department of Neurology | Beth Israel Deaconess Medical Center
330 Brookline Avenue, 02215 Boston, MA, USA
Phone Nr: +1-339-229-7645

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>
Sent: Saturday, May 15, 2021 6:04 PM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Do you need to do that in a common space? The DK is a surface atlas and won’t 
map very accurately to MNI. I think Doug has something for this, but you will 
definitely sacrifice accuracy

Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF)
Sent: Saturday, May 15, 2021 5:56 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas


​Thank you in any case! Do you maybe know if I can enter MNI coordinates in 
freeview and see where it falls into the areas of DK atlas?

Thank you!

Sara


Sara Romanella
Fellow (Ph.D. in Neuroscience)
Berenson-Allen Center for Noninvasive Brain Stimulation
Department of Neurology | Beth Israel Deaconess Medical Center
330 Brookline Avenue, 02215 Boston, MA, USA
Phone Nr: +1-339-229-7645

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>

Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

[Glasser, Matthew]

External Email - Use Caution

Why not go directly surface to surface?  You lose an enormous amount of 
precision going to the volume 
(https://secure-web.cisco.com/129h7FK-zYnFPmjtoOZBCeExQUX7Akm5719AvgT3P9OynVehg_z4G1zvN7diSyupIWwn1aQ5CqNf2zDndOqo1ZJSDghdY1ykv0Aun3SdIa1CRmTMAB-Jo1bzPxJN7Ik3y5KdHQjImgJSxNUXbDTJ7Zet6e4VOjvy6mGat06Wee3ZSDCeQwE7fU-B5TIKCnbYozUX_jUUfz3g3LWyzAtHd2SUKEW85uHqppIyqzPTNq6pzpXjt1Ty5qrU7f_dhFlv5RjfJpslPZpNIrhDu3G9elw/https%3A%2F%2Fwww.pnas.org%2Fcontent%2F115%2F27%2FE6356.short).

Matt.

From:  on behalf of "Romanella,Sara 
(BIDMC - Wilkinson - Neurology SF)" 
Reply-To: Freesurfer support list 
Date: Sunday, May 16, 2021 at 8:47 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas





Hi Matt and Bruce,

Thank you for answering me. I understand. Actually it is simpler than that. I 
have MNI coordinates of the surface resulting from a computational study and I 
need to see where they fall in the areas of the DK atlas. Do you have any 
suggestion?



About Connectome Workbench I was asking for a different project. I was hoping 
to map the entire Brodmann atlas on fsaverage but Bruce kindly advised me it is 
not possible for now.

Thank you.


Sara Romanella
Fellow (Ph.D. in Neuroscience)
Berenson-Allen Center for Noninvasive Brain Stimulation
Department of Neurology | Beth Israel Deaconess Medical Center
330 Brookline Avenue, 02215 Boston, MA, USA
Phone Nr: +1-339-229-7645

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Glasser, Matthew 

Sent: Sunday, May 16, 2021 9:38 PM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas


External Email - Use Caution
One reason Bruce may be asking why you need MNI coordinates is that MNI 
coordinates are a very poor substitute for surface-based statistical maps and a 
terrible way to compare across subjects.  It’s much better to align subjects on 
the surface and then make much more accurate comparisons.  If you have volume 
coordinates from an individual subject, you can project those accurately onto 
that subject’s cortical surface.  In Connectome Workbench we do this with Foci, 
but I bet FreeSurfer has something similar.  You just need to ensure that the 
coordinates and the surface are in the same volume space (i.e. are aligned with 
eachother).  This could be in the subject’s physical space or MNI space (keep 
in mind that FreeSurfer never puts surfaces in MNI space, but we make copies of 
them there in the HCP Pipelines).

I also see you asked how to convert .mgh to a Connectome Workbench readable 
format.  I must admit I’m not entirely sure what .mgh contains.  If it is a 
value per vertex, you could likely use mris_convert to do the conversion to 
.func.gii.  .annot can be converted to .label.gii with mris_convert.

Matt.

From:  on behalf of "Fischl, Bruce" 

Reply-To: Freesurfer support list 
Date: Sunday, May 16, 2021 at 7:34 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas


Hi Sara

Why do you need MNI coordinates at all?

Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Romanella,Sara (BIDMC - 
Wilkinson - Neurology SF)
Sent: Sunday, May 16, 2021 5:57 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas


Hi Bruce,

I can convert the MNI coordinates to subject space. But how do I enter them in 
freeview when I open the DK atlas of the subject to see where they fall?

thank you for the help!


Sara Romanella
Fellow (Ph.D. in Neuroscience)
Berenson-Allen Center for Noninvasive Brain Stimulation
Department of Neurology | Beth Israel Deaconess Medical Center
330 Brookline Avenue, 02215 Boston, MA, USA
Phone Nr: +1-339-229-7645

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>
Sent: Sunday, May 16, 2021 10:31 AM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Hi Sara

Why do you need MNI at all? Why not just do it in individual subject space?
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF)
Sent: Saturday, May 15, 2021 8:43 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas


I am actually not sure. I have some MNI coordinates for the GM surface and I 
should check if they fall into a specific area of the DK. I could sacrifice 
accuracy in order to check this.

Could you please me tell me how if

Re: [Freesurfer] PVC to calculate myelin maps

[Glasser, Matthew]

External Email - Use Caution

I would use the HCP Pipelines for this.

Matt.

From:  on behalf of Marina Fernández 

Reply-To: Freesurfer support list 
Date: Friday, May 28, 2021 at 9:25 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] PVC to calculate myelin maps



External Email - Use Caution
Dear experts,

I want to calculate myelin maps using the ratio of T1w and T2w MRI images. I 
saw that the correction of partial volume effects can be used to create the 
maps (Shafee, Buckner & Fischl, 2015)*.
Can I use the PVC functions of PetSurfer for this purpose? And in case I can:
Should I apply PVC only on T1? Or also in T2?
Which T1 should I use? The original T1 or the T1 with corrections (for example, 
the nu.mgz file that is corrected for variations in intensity)?
Any other advice for calculating myelin maps would be welcome.
Thank you in advance,
Marina

*Link:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1u63hhRf89DUCFEbAiJgcglonczMMzDanUvnXz0DR2W2P39ddbeTTd8zOdP-ChfOveA6XCFA9OL0oSXezE1e96Zfb3KxYR2LDlW-jMoaOoDyQzXJ1Go8H55H3p9wb-PUnVAgkSARhLETfdcQE1Jy3gqRrJtBfJp0CHVh3heFHtl4qp4F98--n6sY0supjb4IKVTOS7yXscz0-PWIge3FA_BDxgUHKOMICIqgiNYDKcVpC3Hr1WYj-GctL7TMtCW-fB7qAj4t3Gaf-ErOb_DKx5g/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4262571%2F%23R48


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Re: [Freesurfer] PVC to calculate myelin maps

[Glasser, Matthew]

External Email - Use Caution

The specific volume to surface mapping we do in the HCP Pipelines minimizes the 
partial volume effects.

Matt.

From:  on behalf of Marina Fernández 

Reply-To: Freesurfer support list 
Date: Friday, May 28, 2021 at 10:06 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] PVC to calculate myelin maps



External Email - Use Caution
Hi Matt,

Thank you very much for the quick answer.

We have our data analyzed with another pipeline that also uses Freesurfer 
functions. For this reason we prefer to calculate myelin maps outside of the 
HCP Pipelines.

Do you think the way of calculating the maps that I explained in the previous 
question is evenly valid?

Best wishes,
Marina






%%%%%



Glasser, 
Matthew<https://secure-web.cisco.com/1EkIb4RUBbvp4aaCzTKvZqXi5mpWtbK6dEiwb2GFTBe5yhOUyifO_hV_E7W1QbzRQK0FwD5cE3KcRI74D3Ovox656ePedxamjtVAEW4AgL4A-7CpFTGP6z5Tq41NoOZ1ojD9zFUJk5ThErtAOajuSKZWvKvti9tqMIHF1q6hCwGlKHevaGmbXlNhh9Qy7R3bO5NIgNuF-fVDEzMvEnu0zjfgN_OsOBclQQKnAUOgbQN0YXzNIZrmOblbk3L2t_TpeCz4wAM71ypty2rwIPsMJYA/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Glasser%252C%2BMatthew%2522>
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External Email - Use Caution



I would use the HCP Pipelines for this.

Matt.




%%%

Marina 
Fernández<https://secure-web.cisco.com/1jnEmX8pyslFDNAKq1ESVKhaVYgavR5DWrZDCQVw6EIjIeRPu8VsMW2BmjjGD5q-TEhUnOvxdrLSTT5-Y6k0YXgDL7svI9z3nYXjvFbLZ7RTupBSGPm81_9ITZGgKJJOgPJdln72nUn8_i_M0BwX5vAQJhvU59P4tJ425dDyWnDLjXoT8Isqf8qqqez-ioXBS40q0Uny8MDDL0kBndUynxMfDLd8eLFxK2zhH_m6k3AE0fJN7n9AYbodo3QU0dDBjU5tlYbAcURsJL_uHxBtJ5Q/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Marina%2BFern%25C3%25A1ndez%2522>
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External Email - Use Caution



Dear experts,

I want to calculate myelin maps using the ratio of T1w and T2w MRI images.

I saw that the correction of partial volume effects can be used to create

the maps (Shafee, Buckner & Fischl, 2015)*.



Can I use the PVC functions of PetSurfer for this purpose? And in case I

can:



Should I apply PVC only on T1? Or also in T2?



Which T1 should I use? The original T1 or the T1 with corrections (for

example, the nu.mgz file that is corrected for variations in intensity)?



Any other advice for calculating myelin maps would be welcome.



Thank you in advance,



Marina





*Link:



https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsOZ5T86whDDL8Q-4ZOYG7rMgwoBYIyC4d5BsThH9nR2UT-_82NU3WKyCZrii6txF4QxCWh-K6Hy6aC2vsOwRupJhTnA_Menjtq1hXOSwjndsWxN3BBnw625eBs0OgB8t1ZM0uY7sLR_VuAuMcsvNsQQ9qofNHMaLp6aidYJh3yhta2kwGeWzCXmtyE1XOS-Z2uiDZa5gqmp9A0egHtAOC68aEN1v8l0S-ikEhif20Qg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4262571%2F%23R48








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Re: [Freesurfer] bias field correction and intensity normalization

[Glasser, Matthew]

External Email - Use Caution

I respond somewhat with trepidation given that you did not take my advice 
previously; however, in case anyone else is wondering—I would not do this.  In 
the absence of head motion, the T1w/T2w ratio will exactly cancel the receive 
field and will attenuate the transmit field (more on this very soon).  
Algorithmic bias correction generally assumes that tissues are homogeneous in 
intensity (usually white matter), but the whole point of studying T1w/T2w 
cortical myelin maps is to look at the inhomogeneity in grey matter.  White 
matter also has real tissue inhomogeneity in T1w and T2w images, and by bias 
correcting the T1w/T2w map, you would be putting the opposite of the white 
matter pattern into the grey matter.   This confound with bias correction was 
why I developed the T1w/T2w ratio in the first place.

Matt.

From:  on behalf of Marina Fernández 

Reply-To: Freesurfer support list 
Date: Tuesday, June 22, 2021 at 6:50 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] bias field correction and intensity normalization

External Email - Use Caution

Dear experts,

I would like to create myelin maps calculating the T1w/T2w ratio. Should

I apply bias field correction and intensity normalization (i.e., "nu

correction" in the Freesurfer pipeline) to T1w and T2w images separately

before calculating the T1w/T2 ratio?



I applied nu correction to T1w images and worked fine but results were

weird when nu correction was applied applied to T2w images. I am not

sure if nu correction must only be applied to T1w images for this

purpose, or if I have to modify some parameters to apply nu correction

to T2w images.



Thank you in advance for your help.



Best,

Marina


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Re: [Freesurfer] Differences in FLAIR assisted pial segmentation from FS6.0 to FS7.1

[Glasser, Matthew]

External Email - Use Caution

We have seen surface placement issues with FreeSurfer 7.X on HCP data as well, 
which is why we’ve continued to recommend folks use FreeSurfer 6.X with the HCP 
Pipelines for now.  Overall, we’ve found that getting the surface placement 
right is often rather finicky and FreeSurfer version dependent and has in the 
past required either our developer effort or FreeSurfer developer effort or 
both.  I have several ideas on how this could be made more robust, but it may 
be that mris_make_surfaces is not really set up to do things of that sort.

Matt.

From:  on behalf of Fredrik Magnussen 

Reply-To: Freesurfer support list 
Date: Thursday, June 24, 2021 at 4:49 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Differences in FLAIR assisted pial segmentation from 
FS6.0 to FS7.1





   External Email - Use Caution

Dear FreeSurfer experts,

We have processed UKB data with FLAIR assisted pial segmentation using FS7.1.

The results differs quite a lot from using FLAIR assisted pial segmentation in 
FS6.0.

For details please see the reported issue on the freesurfer github page: 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
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 Might be related to another issue reported here (though this is T2w assisted 
pial segmentation): MailScanner has detected a possible fraud attempt from 
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The FS pial segmentation for UKB data is prone to include dura if only T1w data 
is used, so assisting with FLAIR is quite detrimental.

Best regards,
Fredrik Magnussen


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Re: [Freesurfer] Analysing HCP Data in freesurfer

[Glasser, Matthew]

External Email - Use Caution

I’m not sure anyone has tried this yet.  Which data are you trying to analyze?  
I cannot tell from the below what type of data this is.

Matt.

From:  on behalf of Poortata Shirish 
Lalwani 
Reply-To: Freesurfer support list 
Date: Thursday, July 29, 2021 at 10:23 AM
To: Freesurfer support list 
Subject: [Freesurfer] Analysing HCP Data in freesurfer

External Email - Use Caution
Hello,
I am trying to use fsfast to perform 1st level GLM analysis on preprocessed 
data from the HCP-Aging dataset which happens to be in a different space than 
fsaverage. I followed the following steps:

First I smoothed the data which was in dtseries format
wb_command -cifti-smoothing *dtseries.nii 1.27 1.27 COLUMN f.sm3.dtseries.nii 
-left-surface *L.midthickness_MSMAll.32k_fs_LR.surf.gii -right-surface 
*R.midthickness_MSMAll.32k_fs_LR.surf.gii

Then extracted the left/right surface and volume
wb_command -cifti-separate f.sm3.dtseries.nii COLUMN -metric CORTEX_LEFT  
f.L.func.gii -metric CORTEX_RIGHT f.R.func.gii -volume-all f.mni152.nii

Followed by creating a mask for the subcortical analysis
mri_binarize --i Atlas_ROIs.2.nii.gz --match  81011121316   
 17182628474950515253  545860 --o 
subcortmask.nii.gz;

and creating a global mean .dat file.
wb_command -cifti-stats f.sm3.dtseries.nii -reduce MEAN > global.waveform.dat

Then I tried to run GLM analysis using FSFast. The subcortical analysis 
completes without errors, but I am having trouble with the surfaces.

Surprisingly, the error seems to be at the Smoothing ACF step because it is 
trying to perform it on volume even though I have specified that the analysis 
should be in surface space. Attached are the selx3 log file and analysis info 
file. Is there something with the analysis specification or in earlier 
conversion steps? I would appreciate any help with this.
Thank you

Best,
Pia


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Re: [Freesurfer] Analysing HCP Data in freesurfer

[Glasser, Matthew]

External Email - Use Caution

It might be easier to use the HCP’s TaskAnalysis Pipeline (of which there will 
be a new version in the master development branch shortly that has improvements 
for the HCP Lifespan projects), as that is designed to work directly with the 
other outputs of the HCP Pipeline.  It is correct that we recommend starting 
from the cleaned and MSMAll aligned functional MRI data:

${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp0_clean.dtseries.nii

It would be nice to support fsfast also as it is a surface-based approach, but 
I don’t personally have any experience with fsfast.  Thus far, the FSL 
developers have been most engaged in supporting CIFTI with their tools (and the 
HCP’s task analysis pipeline is based on FSL’s FEAT), but I would be happy to 
work with the FreeSurfer developers to figure out the best way for users to 
process CIFTI data with fsfast if there is a mutual interest in this.

Matt.

From:  on behalf of Poortata Shirish 
Lalwani 
Reply-To: Freesurfer support list 
Date: Thursday, July 29, 2021 at 11:39 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Analysing HCP Data in freesurfer

External Email - Use Caution
I am trying to analyse the HCP-Aging vismotor task fMRI 
data<https://secure-web.cisco.com/1Z30FmBulf3wPk8ZI1piszdCtNxfv_oM8hAju_21Q2rqxpYuGRsbRPC84dN3sp47oBdJLeOU7T9szqn8hcIkH4BhLhOBGhJvd5XLqntcuUFtPaWurM0LgbDUCjvps3yPQB_EvdAfv_Ao-NgAp8KZNUYyv4AybUV5-WXbC3PjGeQIaj7FgDLIVaKTIx1Snw558T4Vnz72IWqJurISu__OS0h5zc-uKdjgeB4bPhvloeUMkY57oe6VxBLQ93zhlWAyKpxdlrKxLcu1BnxApRJa6kA/https%3A%2F%2Fwww.humanconnectome.org%2Fstudy%2Fhcp-lifespan-aging%2Fproject-protocol%2Ftask-protocols-hcp-aging>
 with an event-based design. The provided file is dtseries.nii format and is 
the recommended starting point for tfMRI analyses by HCP-Aging. The cleaned 
file is precisely aligned across subjects using the MSMAll multimodal surface 
registration and is created applying GenericfMRIVolumeProcessingPipeline, 
GenericfMRISurfaceProcessingPipeline, hcp_fix_multi_run, and MSMAllPipeline. I 
was hoping to simply run GLM analysis on this file in fsfast but I am not sure 
which files the smoothing function is searching for since it is surface-based 
analysis.

On Thu, Jul 29, 2021 at 10:29 AM Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

External Email - Use Caution
I’m not sure anyone has tried this yet.  Which data are you trying to analyze?  
I cannot tell from the below what type of data this is.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Poortata Shirish Lalwani 
mailto:poort...@umich.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, July 29, 2021 at 10:23 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Analysing HCP Data in freesurfer

External Email - Use Caution
Hello,
I am trying to use fsfast to perform 1st level GLM analysis on preprocessed 
data from the HCP-Aging dataset which happens to be in a different space than 
fsaverage. I followed the following steps:

First I smoothed the data which was in dtseries format
wb_command -cifti-smoothing *dtseries.nii 1.27 1.27 COLUMN f.sm3.dtseries.nii 
-left-surface *L.midthickness_MSMAll.32k_fs_LR.surf.gii -right-surface 
*R.midthickness_MSMAll.32k_fs_LR.surf.gii

Then extracted the left/right surface and volume
wb_command -cifti-separate f.sm3.dtseries.nii COLUMN -metric CORTEX_LEFT  
f.L.func.gii -metric CORTEX_RIGHT f.R.func.gii -volume-all f.mni152.nii

Followed by creating a mask for the subcortical analysis
mri_binarize --i Atlas_ROIs.2.nii.gz --match  81011121316   
 17182628474950515253  545860 --o 
subcortmask.nii.gz;

and creating a global mean .dat file.
wb_command -cifti-stats f.sm3.dtseries.nii -reduce MEAN > global.waveform.dat

Then I tried to run GLM analysis using FSFast. The subcortical analysis 
completes without errors, but I am having trouble with the surfaces.

Surprisingly, the error seems to be at the Smoothing ACF step because it is 
trying to perform it on volume even though I have specified that the analysis 
should be in surface space. Attached are the selx3 log file and analysis info 
file. Is there something with the analysis specification or in earlier 
conversion steps? I would appreciate any help with this.
Thank you

Best,
Pia


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immediately notify 

Re: [Freesurfer] Analysing HCP Data in freesurfer

[Glasser, Matthew]

External Email - Use Caution

Like I said before, the HCP has a task analysis pipeline written specifically 
for CIFTI (and FSL also has CIFTI enabled tools).  
https://secure-web.cisco.com/16-PqNZ69sCQhtOyBAv6e4grcj8m_fit1m4rcGKVXpOrLNVugaZo3icg0pLBSV4wtun0b4kmIikMHHHnTTJ7vO1EHem-hIoujNWBxSlJ30hgliCDTAjse7ynaaSJ0_zENeFeTnpx1U5M0vk6Vm5vHlw-UWhHaveKjv14mj99lDc67AKfXabxEuoywh3rH3XnOo8WQm_7IHtXEEeGL8raiZ76ZsLZUfbL_j1-ulO04Mzaqf3cqMwu-W8VswfCB7FzwP3a9VSoY0ToeI_pWG6_m6g/https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Ftree%2Fmaster%2FTaskfMRIAnalysis

We will be merging in a new version in the next few days.

Matt.

From:  on behalf of Poortata Shirish 
Lalwani 
Reply-To: Freesurfer support list 
Date: Friday, July 30, 2021 at 7:43 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Analysing HCP Data in freesurfer



External Email - Use Caution
I wanted to perform event related analysis of the task fmri data but create my 
own design file for the analysis. Also I do prefer to do it in surface space.

I have been able to use FSL for task fmri analysis on the unprocessed raw 
volume file and run event related analysis on the HCP young dataset by 
modifying the HCP pipeline. But wasn't able to find a straight forward way to 
do so with HCP lifespan dataset using the recommended aligned files. FSL can't 
open the dtseries.nii file so I am guessing it needs something else? If you can 
share the code that can do glm fitting and cope estimation in surface space for 
the lifespan data (assuming I just didn't locate it right), that would be 
immensely helpful.

Relatedly, my understanding is that this should be straightforward even in 
freesurfer since it is simple glm fitting. I figured all the necessary files 
are already created for the HCP data and it is just a matter of renaming files 
and modifying the directory structure in a way Freesurfer prefers. But maybe 
not? I am not sure what files the smoothing function is looking for. I do think 
it would be really useful for many other users to be able to work with HCP data 
in freesurfer. Thanks for your help in doing this.


Best,
Pia

On Thu, Jul 29, 2021, 11:48 AM Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

External Email - Use Caution
It might be easier to use the HCP’s TaskAnalysis Pipeline (of which there will 
be a new version in the master development branch shortly that has improvements 
for the HCP Lifespan projects), as that is designed to work directly with the 
other outputs of the HCP Pipeline.  It is correct that we recommend starting 
from the cleaned and MSMAll aligned functional MRI data:

${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp0_clean.dtseries.nii

It would be nice to support fsfast also as it is a surface-based approach, but 
I don’t personally have any experience with fsfast.  Thus far, the FSL 
developers have been most engaged in supporting CIFTI with their tools (and the 
HCP’s task analysis pipeline is based on FSL’s FEAT), but I would be happy to 
work with the FreeSurfer developers to figure out the best way for users to 
process CIFTI data with fsfast if there is a mutual interest in this.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Poortata Shirish Lalwani 
mailto:poort...@umich.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, July 29, 2021 at 11:39 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Analysing HCP Data in freesurfer

External Email - Use Caution
I am trying to analyse the HCP-Aging vismotor task fMRI 
data<https://secure-web.cisco.com/1Z30FmBulf3wPk8ZI1piszdCtNxfv_oM8hAju_21Q2rqxpYuGRsbRPC84dN3sp47oBdJLeOU7T9szqn8hcIkH4BhLhOBGhJvd5XLqntcuUFtPaWurM0LgbDUCjvps3yPQB_EvdAfv_Ao-NgAp8KZNUYyv4AybUV5-WXbC3PjGeQIaj7FgDLIVaKTIx1Snw558T4Vnz72IWqJurISu__OS0h5zc-uKdjgeB4bPhvloeUMkY57oe6VxBLQ93zhlWAyKpxdlrKxLcu1BnxApRJa6kA/https%3A%2F%2Fwww.humanconnectome.org%2Fstudy%2Fhcp-lifespan-aging%2Fproject-protocol%2Ftask-protocols-hcp-aging>
 with an event-based design. The provided file is dtseries.nii format and is 
the recommended starting point for tfMRI analyses by HCP-Aging. The cleaned 
file is precisely aligned across subjects using the MSMAll multimodal surface 
registration and is created applying GenericfMRIVolumeProcessingPipeline, 
GenericfMRISurfaceProcessingPipeline, hcp_fix_multi_run, and MSMAllPipeline. I 
was hoping to simply run GLM analysis on this file in fsfast but I am not sure 
which files the smoothing function is searching for since it is surface-based 
analysis.

On Thu, Jul 29, 2021 at 10:29 AM Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

External Email - Use Caution
I’m not sure anyone has tried this yet.  Which data are you trying to analyze?  
I cannot tell from the below what ty

Re: [Freesurfer] Analysing HCP Data in freesurfer

[Glasser, Matthew]

External Email - Use Caution

The updated version of this pipeline is now available in the master branch and 
will be what we will use for the official lifespan task fMRI analysis.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Friday, July 30, 2021 at 7:43 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Analysing HCP Data in freesurfer



External Email - Use Caution
Like I said before, the HCP has a task analysis pipeline written specifically 
for CIFTI (and FSL also has CIFTI enabled tools).  MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1Kx4v4Z0ry1cLWDjWWA0GB-gQ-GbOk7O82thSRoypDsSzhJwibsC7kAoZpSpy8LREYP0c2eyFJFV3w2vpJSuneVRC3JRAOwPDIoG2b6NJkU6sHFKdDC0uxL1taeXlTBEt9XbMY3KVhXLqzMJVBDi8CvKwqYLTY5szauFwBwWsuezaN3KUiEeb2Xld3tJwT5w8Uy4uI-_1o1Yp0ILOZVhQyOjnz6Taux_W-846uDx_2XKd5KUsg634-82y-dURTLuDpBPkeb827QpPFWGZ5aMiNg/https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Ftree%2Fmaster%2FTaskfMRIAnalysis<https://secure-web.cisco.com/16-PqNZ69sCQhtOyBAv6e4grcj8m_fit1m4rcGKVXpOrLNVugaZo3icg0pLBSV4wtun0b4kmIikMHHHnTTJ7vO1EHem-hIoujNWBxSlJ30hgliCDTAjse7ynaaSJ0_zENeFeTnpx1U5M0vk6Vm5vHlw-UWhHaveKjv14mj99lDc67AKfXabxEuoywh3rH3XnOo8WQm_7IHtXEEeGL8raiZ76ZsLZUfbL_j1-ulO04Mzaqf3cqMwu-W8VswfCB7FzwP3a9VSoY0ToeI_pWG6_m6g/https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Ftree%2Fmaster%2FTaskfMRIAnalysis>

We will be merging in a new version in the next few days.

Matt.

From:  on behalf of Poortata Shirish 
Lalwani 
Reply-To: Freesurfer support list 
Date: Friday, July 30, 2021 at 7:43 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Analysing HCP Data in freesurfer



External Email - Use Caution
I wanted to perform event related analysis of the task fmri data but create my 
own design file for the analysis. Also I do prefer to do it in surface space.

I have been able to use FSL for task fmri analysis on the unprocessed raw 
volume file and run event related analysis on the HCP young dataset by 
modifying the HCP pipeline. But wasn't able to find a straight forward way to 
do so with HCP lifespan dataset using the recommended aligned files. FSL can't 
open the dtseries.nii file so I am guessing it needs something else? If you can 
share the code that can do glm fitting and cope estimation in surface space for 
the lifespan data (assuming I just didn't locate it right), that would be 
immensely helpful.

Relatedly, my understanding is that this should be straightforward even in 
freesurfer since it is simple glm fitting. I figured all the necessary files 
are already created for the HCP data and it is just a matter of renaming files 
and modifying the directory structure in a way Freesurfer prefers. But maybe 
not? I am not sure what files the smoothing function is looking for. I do think 
it would be really useful for many other users to be able to work with HCP data 
in freesurfer. Thanks for your help in doing this.


Best,
Pia

On Thu, Jul 29, 2021, 11:48 AM Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

External Email - Use Caution
It might be easier to use the HCP’s TaskAnalysis Pipeline (of which there will 
be a new version in the master development branch shortly that has improvements 
for the HCP Lifespan projects), as that is designed to work directly with the 
other outputs of the HCP Pipeline.  It is correct that we recommend starting 
from the cleaned and MSMAll aligned functional MRI data:

${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp0_clean.dtseries.nii

It would be nice to support fsfast also as it is a surface-based approach, but 
I don’t personally have any experience with fsfast.  Thus far, the FSL 
developers have been most engaged in supporting CIFTI with their tools (and the 
HCP’s task analysis pipeline is based on FSL’s FEAT), but I would be happy to 
work with the FreeSurfer developers to figure out the best way for users to 
process CIFTI data with fsfast if there is a mutual interest in this.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Poortata Shirish Lalwani 
mailto:poort...@umich.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, July 29, 2021 at 11:39 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Analysing HCP Data in freesurfer

External Email - Use Caution
I am trying to analyse the HCP-Aging vismotor task fMRI 
data<https://secure-web.cisco.com/1Z30FmBulf3wPk8ZI1piszdCtNxfv_oM8hAju_21Q2rqxpYuGRsbRPC84dN3sp47oBdJLeOU7T9szqn8hcIkH4BhLhOBGhJvd5XLqntcuUFtPaWurM0LgbDUCjvps3yPQB_EvdAfv_Ao-NgAp8KZNUYyv4AybUV5-WXbC3PjGeQIaj7FgDLIVaKTIx1Snw558T4Vnz72IWqJurISu__OS0h5zc-uKdjgeB4bPhvloeUMkY57oe6VxBLQ93zhlWAyKpxdlrKxLcu1BnxApRJa6kA/ht

Re: [Freesurfer] Error During T2/FLAIR Pial Surface Refinement

[Glasser, Matthew]

External Email - Use Caution

2D thick slice images are not appropriate for surface generation.

Matt.

From:  on behalf of Thomas Kaufmann 

Reply-To: Freesurfer support list 
Date: Tuesday, October 29, 2024 at 1:46 PM
To: "Freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Error During T2/FLAIR Pial Surface Refinement

External Email - Use Caution
Hi Bruce,

Thanks for your response. I figured it out, but it took a while to 
troubleshoot. There were a number of issues at play, some due to my stupidity 
and some that may suggest feature improvements.

  1.  The primary issue was that the FOV of the T2 images did not cover the 
entire brain volume, presumably since the primary purpose of the acquisition 
was to inspect the ventricles and/or subcortical structures.
  2.  In this scenario, the current stable release appears to exit with the 
"Segmentation fault" error as described in my original message. The current dev 
version spits out the "MRIhistogramLabelRegion: constant image" error and then 
just hangs indefinitely with 100% CPU load.
  3.  It may be a good idea to implement a check at the beginning of recon-all 
(if a T2 or FLAIR flag is passed) to verify if the image contains the entire 
brain volume. If it doesn't, an error message could be raised, so the user has 
an opportunity to correct their mistake.
  4.  Once I realized the issue, I exported a different image sequence that 
contained the full brain volume. I then ran -autorecon3 with the new T2 image, 
but the process still failed. This is where I got stuck for HOURS. The reason 
for the fault was that the transforms for the T2 image from the previous T2 
image are retained in the mri/transforms folder. Therefore, the transforms of 
the incomplete images were applied to the complete images, resulting in 
cropping of the brain volume to the point where it was then incomplete again. 
This ultimately led to the same problem. The mri/orig/T2raw.mgz image was in 
good shape, but the mri/T2.mgz would already exhibit the cropping.
  5.  It may be a good idea to implement a check that verifies whether the T2 
image has changed and if the existing transforms correspond to the specified T2 
image, possibly via a checksum that is stored in the 
T2raw.auto.*
 and/or the T2raw.lta file. If it is determined that the input image has been 
updated and does not correspond to the transforms, the automatically generated 
transforms could be overwritten, thereby avoiding this issue. Or you could just 
recreate the automatic transforms regardless, since it seems that it would only 
be useful to retain transforms if they contain manual or external registration 
data.
  6.  If access to my images or logs would be helpful to you in the (potential) 
implementation of these suggestions, please let me know and I can upload them. 
I retained a copy of one of the problematic folders.
There were a few issues I (may or may not have) encountered along the way. 
Unfortunately, I didn't keep detailed enough notes throughout my 
troubleshooting process and don't have the (compute) time to recreate these 
potential problem areas. It may be a good idea to verify if the following items 
cause problems:

  1.  I originally called recon-all with the -T2 flag, but did not include 
-T2pial. I don't recall if this created an issue or if the -T2pial flag is 
implied when passing a T2 image. Presumably, this behavior would be analogous 
for FLAIR images.
  2.  I worked with the -parallel -openmp N flag for a while and then suspected 
that this may have been part of the problem. I believe to remember that when 
using the -parallel flag, all of my T2 processing failed, while only the ones 
with incomplete image volumes failed when not using the -parallel flag.
  3.  I have one image series with 512 x 512 x 170 px dimensions and a FOV of 
260 degrees. FreeSurfer is not happy about that. I tried to use -hires and 
-cw256 (which appear to be mutually exclusive). I eventually ended up simply 
cropping it with MRIcroGL. It would be nice to have an automatic feature in 
FreeSurfer that crops excessive FOVs, so that this glitch doesn't occur and 
this manual step wouldn't be necessary. It would also be helpful to have the 
option in mri_convert to specify both the crop size and the center of a crop. 
Currently, these options appear to be mutually exclusive.
  4.  Most of my T1 images are 256 x 256 px in size, but the T2 images are all 
higher resolution, either 384 x 384 or 512 x 512, but with a very large slice 
thickness of more than 4 mm. I don't know if it's possible and how it's 
current