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
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,
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. Gr
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:Fr
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 simi
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:
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@nm
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
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.harva
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: T
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...@gm
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, O
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: Freesurf
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 e
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
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@n
hink 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
n, 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 Emai
on, 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 b
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 o
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
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
>wor
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: Mon
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 a
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, 2
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
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
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
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 us
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
w 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 you
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
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
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. i
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 area
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
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
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 coordinate
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: "fr
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, Janua
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
Subjec
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: Fre
er@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.
>&g
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 free
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 Jo
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 FreeSu
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 do
urfile.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 Fre
ught 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 - U
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 s
fan 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: Freesurfe
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 beh
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:
son 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: 0292
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 const
.
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
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
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"
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
-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...@wust
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 s
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}/MNINon
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 surfa
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
${StudyFolde
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:
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
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
enefit 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:
ruce
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
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-As
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] argumen
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"
Subjec
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: "fre
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"
Subje
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 s
ary 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
n 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:
&
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
.
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
son 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: Free
--
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 ${S
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 2.6m
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,
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
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@
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 par
nce.
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 Fernánd
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 supp
...@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_
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 th
9-229-7645
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
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
ps 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-
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 atte
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
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, 2
ti_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:
k 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
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
Da
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]
1 - 100 of 101 matches
Mail list logo
