[Freesurfer] Brain Imaging, Built Better: The HCP Course in Hawaii

[Matt Glasser]

To advance the field of brain imaging, the HCP was given the unusual NIH
mandate to devote its first two years to rethinking data acquisition and
analysis methods prior to collecting its core dataset.  The HCP course
provides an excellent opportunity for brain imagers to profit from this
experience by interacting with key HCP investigators in an accessible and
approachable setting.  Among the speakers are David Van Essen (HCP¹s PI),
Steve Smith (FSL), Tom Nichols (brain imaging statistician), Dan Marcus
(XNAT and ConnectomeDB), Robert Oostenveld (FieldTrip), and many others.

We¹ve designed the HCP Course both for folks with considerable brain
imaging experience and for those who are just starting out.  Attendees
will learn how to take advantage of HCP-related advances in data
acquisition, preprocessing, and analysis methods, enhancing their
prospects in an increasingly competitive neuroimaging field.  Highlighted
topics include:

*How to acquire high quality MRI data for use with the HCP¹s cutting-edge
analysis tools.
*How to better answer the question ³Where am I in the brain?² by using the
HCP¹s new standard space and analysis approach‹CIFTI grayordinates‹that
substantially improves spatial localization across subjects and studies.
*How to avoid the erosion of neuroanatomical fidelity caused by
conventional brain imaging analysis methods, instead accurately aligning
cortical areas across subjects and studies and minimizing blurring.
*The first public unveiling of the HCP¹s group average multi-modal
cortical parcellation together with methods for automatically defining
these parcels in individual subjects‹even those with atypical cortical
organization.
*How to perform novel analyses by integrating very high temporal
resolution electrophysiological data (MEG) together with high spatial
resolution MRI in a common analysis framework built around parcellation.

Note that space is limited‹and who doesn¹t want an excuse join us in
Hawaii for an extra week before OHBM? (June 8-12)

See the HCP course website for more details and let us know if you have
any questions (hcpcou...@humanconnectome.org):

http://humanconnectome.org/course-registration/2015/exploring-the-human-con
nectome.php 

Hope to see you in Honolulu,

Matt Glasser.



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Re: [Freesurfer] mris_convert gifti

[Matt Glasser]

Does SUMA support GIFTI and provide a utility to convert between its
formats and GIFTI?  I was also wondering what a .dset was and how to get
it into GIFTI so it could be easily used across software platforms.

Thanks,

Matt.

On 5/5/15, 5:30 PM, "Bruce Fischl"  wrote:

>sorry, I think this may be a question for the SUMA people - I don't know
>what .dset format is. Are you going to do the masking within SUMA? I'll
>cc 
>Ziad so he can chime in.
>
>cheers
>Bruce
>
>On Tue, 5 May 2015, Francesca Strappini wrote:
>
>> I'm trying to mask a time series dataset that I mapped to the surface in
>> SUMA (surface created with freesurfer and imported into SUMA). I think
>>the
>> input should be in the .dset fomat (region mapped to the surface). The
>> problem is that when I save my label the annotation file has only a
>>list of
>> vertexes related to the region and not all the surface vertexes.
>> Thanks for the help!
>> Francesca
>> 
>> 2015-05-05 23:04 GMT+02:00 Bruce Fischl :
>>   you can just create a label file I guess. What input does SUMA
>>   take?
>>   On Tue, 5 May 2015, Francesca Strappini wrote:
>>
>> Sorry, just to be clear, I meant how can I create a
>> mask on the surface in
>> which at each vertex is assigned a value, 0 or 1.
>> I need to create this mask for exporting the
>> freesurfer labels into SUMA and
>> ultimately to extract the time series from each
>> vertex.
>>
>> Thanks
>> Francesca
>>
>> 2015-05-05 16:06 GMT+03:00 Francesca Strappini
>> :
>>   Thank you! Do you know which function should I
>> use?
>>
>> Best
>> Francesca
>>
>> 2015-05-05 15:30 GMT+03:00 Bruce Fischl
>> :
>>   yes, you can use a label for this (we use the
>>   ?h.cortex.label for this purpose routinely to
>> remove
>>   non-cortical stuff)
>>   On Tue, 5 May 2015, Francesca Strappini wrote:
>>
>> Thank you so much! I understand what's
>> the
>> problem and I will make my custom
>> ctab file.
>>
>> Last question, about the annot files, is
>> it
>> possible with freesurfer to
>> create a mask with the annot or the
>> label
>> files in which the value 1 is
>> assigned to the region and 0 to the rest
>> of
>> the brain?
>>
>> Thanks again!
>>
>> Best
>> Francesca
>>
>> 2015-05-05 4:20 GMT+03:00 Nick
>> Schmansky, MGH
>> :
>>   Francesca,
>>
>>   I looked at the files you sent and
>> replicated the problem.  It
>>   is due to
>>   creating your lh.EKppa.annot file
>> using
>> FreeSurferColorLUT.txt
>>   as the
>>   colortable file.  You should
>> create your
>> own colortable file,
>>   which is
>>   simple to do, and create a new
>> .annot
>> file using that colortable
>>   (ie,
>>   the --ctab option in
>> mris_label2annot).
>>
>>   Here is a simple colortable.txt
>> file
>> (just a text file) with
>>   four
>>   entries, which in this example,
>> means
>> that you have three
>>   annotations.
>>   The first entry must be as it is
>> shown,
>> ie, 'unknown', as this
>>   is used
>>   to automatically 'label' all the
>> vertices which do not have a
>>   .label
>>   file.
>>
>> 0  unknown
>>
>> 25   5  250
>> 1  mylabel1
>>
>> 0  92  230
>> 2  mylabel2
>>   131
>> 148 2550
>> 3  mylabel3
>>
>> 0   0 2550
>>
>>   I fixed the code locally

Re: [Freesurfer] Caret Human_Macaque.PALS_B12 to freesurfer

[Matt Glasser]

I agree this would be best asked on the Caret list to begin with (as far
as conversion from Caret formats to FreeSurfer formats), however I don’t
provide Caret support either having not used it in years (I can be more
helpful with Connectome Workbench stuff).  Donna on the Caret list can
perhaps provide further help.

Peace,

Matt.

On 8/13/15, 12:12 PM, "Bruce Fischl"
 wrote:

>Hi Jan
>
>have you asked the HCP/Wash U group? I bet that they would know. Maybe
>Mike 
>Harms or Matt Glasser can chime in?
>Bruce
>
>
>On Thu, 13 
>Aug 2015, Jan Willem Koten wrote:
>
>> 
>> Dear ladies and possibly gentlemen as well,
>> 
>>  
>> 
>> I have got a rather nasty question. I would like to import the following
>> caret file
>> 
>> „Human_Macaque.PALS_B12.RIGHT-DEPTH_Expansion.73730.surface_shape“
>> 
>> into free surfer and bring it into fs average space. In a next step I
>>would
>> like to import the caret/fsaverage result into matlab and do some stuff
>>with
>> it.
>> 
>> There seems to be a mismatch between caret and freesurfer in the vertex
>> numbers. Has somebody every tried this? Can it be done?
>> 
>> I am not familiar with caret and would like to avoid using it.
>>Alternatively
>> there is matlab toolbox for caret. But I have no clue how to get from
>>one
>> ico vertex system into another.
>> 
>>  
>> 
>> Greetings
>> 
>>  
>> 
>> Jan
>> 
>> Jan Willem Koten (van Grevenbicht) Neurological Clinic at the RWTH
>>Aachen
>> Pauwelstraße 30, 52074 Aachen, Germany Telephone: (0049) (0)241 8089909
>> 
>> 
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Re: [Freesurfer] Basic error

[Matt Glasser]

You cannot have spaces in the file name unless you enclose it with quotes.

Peace,

Matt.

From:   on behalf of Hugh Pemberton

Reply-To:  Freesurfer support list 
Date:  Sunday, August 16, 2015 at 1:34 PM
To:  "Freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Basic error

Hi freesurfer team,

I think this is a very basic error with the mri_convert command but I can't
seem to make it work, I'm getting this:

mri_convert $PWD 001.nii

mri_convert /Applications/freesurfer/subjects/DEM009/dicom/20140731/1835
001.nii 

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from 
/Applications/freesurfer/subjects/DEM009/dicom/20140731/1835...

corRead(): can't open file
/Applications/freesurfer/subjects/DEM009/dicom/20140731/1835/COR-.info

Any ideas what I'm missing?
Thanks,
Hugh
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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[Matt Glasser]

I would be interested to know how well 0.7mm isotropic resolution data
performs at hippocampal segmentation.  It would be better if folks could do
this then needing to acquire specialized anisotropic scans for hippocampal
segmentation.

Peace,

Matt.

From:   on behalf of Fernando
Pasquini Santos 
Reply-To:  Freesurfer support list 
Date:  Thursday, June 9, 2016 at 1:23 PM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of the input?

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal
Subfield segmentation in Freesurfer 6.0 -
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the
same standard 1mm T1 image with an additional scan. However, I want to use a
0.7mm T1 image as input, with an additional T2 scan. When I run the program
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm
voxel size. So, I don't know if this happens just because of the recon-all
program or if the segmentation is being done in the downsampled T1 image or
in the original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation
using ex vivo, ultra-high resolution MRI: Application to adaptive
segmentation of in vivo MRI" I saw that, in the methods section, the
algorithm is used to segment 0.6mm T1 images. But is this possible to do in
the Freesurfer package? Obviously, doing the segmentation directly on 0.7mm
data would be better than a downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu
fernando.pasquini.san...@usp.br
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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[Matt Glasser]

Hi Eugenio,

Did you already do this?  If so, a published reference would be more useful
to me than instructions for how to do it, as I¹m more interested in making
an argument for an acquisition protocol modification.

Matt.

From:   on behalf of "Iglesias,
Eugenio" 
Reply-To:  Freesurfer support list 
Date:  Thursday, June 9, 2016 at 1:37 PM
To:  Freesurfer support list 
Subject:  Re: [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of the input?

Hi Matt, 
you can use strategy 3 of my previous email ;-)
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


> On 9 Jun 2016, at 19:31, Matt Glasser  wrote:
> 
> I would be interested to know how well 0.7mm isotropic resolution data
> performs at hippocampal segmentation.  It would be better if folks could do
> this then needing to acquire specialized anisotropic scans for hippocampal
> segmentation.
> 
> Peace,
> 
> Matt.
> 
> From:  on behalf of Fernando Pasquini
> Santos 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 9, 2016 at 1:23 PM
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Subject: [Freesurfer] Hippocampal subfields segmentation - what is the voxel
> size of the input?
> 
> Dear,
> 
> I have a doubt regarding the input T1 image used for the Hippocampal Subfield
> segmentation in Freesurfer 6.0 -
> https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
> 
> In this documentation it says that I can use a standard 1mm T1 image or the
> same standard 1mm T1 image with an additional scan. However, I want to use a
> 0.7mm T1 image as input, with an additional T2 scan. When I run the program
> with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel
> size. So, I don't know if this happens just because of the recon-all program
> or if the segmentation is being done in the downsampled T1 image or in the
> original 0.7mm.
> 
> By reading the article "A computational atlas of the hippocampal formation
> using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation
> of in vivo MRI" I saw that, in the methods section, the algorithm is used to
> segment 0.6mm T1 images. But is this possible to do in the Freesurfer package?
> Obviously, doing the segmentation directly on 0.7mm data would be better than
> a downsampled version to 1mm...
> 
> Thanks,
> 
> Fernando Pasquini Santos
> PhD student in Dynamic Systems
> fernandosan...@pitt.edu
> fernando.pasquini.san...@usp.br
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> 
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> addressed. If you believe this e-mail was sent to you in error and the e-mail
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> at
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Re: [Freesurfer] using both T1/T2 and resolutions

[Matt Glasser]

Hi Jim,

I would just use the HCP Pipelines for that:
https://github.com/Washington-University/Pipelines, as they take care of all
of those things re FreeSurfer.  I would set to using the 0.8mm templates so
that nothing is down sampled.

Peace,

Matt.

From:   on behalf of "Alexopoulos,
Dimitrios" 
Reply-To:  Freesurfer support list 
Date:  Friday, June 10, 2016 at 10:56 AM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] using both T1/T2 and resolutions

Hi,
 
We¹d like to process pediatric data through the complete FS 5.3 pipeline.
The T1/T2 data are acquired with a 3T Siemens as follows:
T1 mpr sag - 0.82x0.82x0.85
T2 Space - 1x1x1
 
We¹d like to process using both the T1 and T2 (for better dura removal and
possible myelin analysis).
Is it possible to use the hires T1 and have data not downsampled to 1x1x1?
Ifpossible, can this be done in tandem with the lower resolution T2-space?
 
What recon-all command would be best for this process?
 
Jim


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Re: [Freesurfer] using both T1/T2 and resolutions

[Matt Glasser]

Hi Eugenio,

I think he is just after cortical surfaces.

Matt.

From:   on behalf of "Iglesias,
Eugenio" 
Reply-To:  Freesurfer support list 
Date:  Friday, June 10, 2016 at 12:30 PM
To:  Freesurfer support list 
Subject:  Re: [Freesurfer] using both T1/T2 and resolutions

Hi! 
I actually sent out an email yesterday regarding this. The way that the
subfield module is set up, you cannot take advantage of your full res T1 and
your T1. We are working on a solution.
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


> On 10 Jun 2016, at 17:04, Matt Glasser  wrote:
> 
> Hi Jim,
> 
> I would just use the HCP Pipelines for that:
> https://github.com/Washington-University/Pipelines, as they take care of all
> of those things re FreeSurfer.  I would set to using the 0.8mm templates so
> that nothing is down sampled.
> 
> Peace,
> 
> Matt.
> 
> From:  on behalf of "Alexopoulos,
> Dimitrios" 
> Reply-To: Freesurfer support list 
> Date: Friday, June 10, 2016 at 10:56 AM
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Subject: [Freesurfer] using both T1/T2 and resolutions
> 
> Hi,
>  
> We¹d like to process pediatric data through the complete FS 5.3 pipeline. The
> T1/T2 data are acquired with a 3T Siemens as follows:
> T1 mpr sag - 0.82x0.82x0.85
> T2 Space - 1x1x1
>  
> We¹d like to process using both the T1 and T2 (for better dura removal and
> possible myelin analysis).
> Is it possible to use the hires T1 and have data not downsampled to 1x1x1?
> Ifpossible, can this be done in tandem with the lower resolution T2-space?
>  
> What recon-all command would be best for this process?
>  
> Jim
> 
> 
> The materials in this email are private and may contain Protected Health
> Information. If you are not the intended recipient, be advised that any
> unauthorized use, disclosure, copying, distribution 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 email.
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> 
> 
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> at
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Re: [Freesurfer] Fwd: concerting surface format

[Matt Glasser]

Look at mris_convert.  If that doesn¹t help would also see if BrainVisa
allows conversion to a third format that mris_convert works with.  Finally,
does BrainVisa not support GIFTI (the standard, cross-neuroimaging software
surface format)?

Peace,

Matt.

From:   on behalf of Trisanna
Sprung-Much 
Reply-To:  Freesurfer support list 
Date:  Wednesday, June 15, 2016 at 9:33 AM
To:  Freesurfer support list 
Subject:  [Freesurfer] Fwd: concerting surface format



Hi there

is there a way to convert .mesh (BrainVisa) to the Freesurfer surface
format? mri_convert doesn't seem to do it.

best wishes

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology



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Re: [Freesurfer] modifying files on older versions of FS

[Matt Glasser]

Why would  you want to do that?

Peace,

Matt.

From:   on behalf of "Alexopoulos,
Dimitrios" 
Reply-To:  Freesurfer support list 
Date:  Thursday, June 16, 2016 at 4:06 PM
To:  Freesurfer support list 
Subject:  [Freesurfer] modifying files on older versions of FS

I have successfully processed data with FS v5.3 (linux/CentOS) using
recon-all -all.
 
Is it possible to make modifications to the 5.3-generated brainmask.mgz
(primarily dura removal) and wm.mgz files using a much older 4.4 version of
FS and then re-run recon-all on 5.3 with these modified files. I¹d also be
generating control points (control.dat file) on 4.4 as well.
 
In other works are there file formatting differences between these FS
versions for just these 3 files that could pose a problem when re-running
the dataset.
 
Jim


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Re: [Freesurfer] FreesurferNHP

[Matt Glasser]

We haven¹t yet released our NHP pipeline yet, mainly because the software
support requirements are a bit higher and so it has made more sense to
work with people as a part of collaborations.  This is more of a question
for the HCP Users list or an off-list inquiry because the FreeSurfer group
doesn¹t have anything to do with the FreeSurferNHP pipeline.

Peace,

Matt.

On 7/12/16, 9:17 AM, "Moeller, Sebastian"
 wrote:

>Hi Peter,
>
>> On Jul 12, 2016, at 14:42 , Lauro, Peter  wrote:
>> 
>> Hello,
>> 
>> I'm trying to reconstruct cortical surfaces from non-human primate
>>MRIs. I tried following the instructions/scripts listed here
>>(https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData), but I was unable
>>to make it work (I¹m also running FS 5.3).
>
>   What went wrong?
>
>Best Regards
>   Sebastian
>
>> I noticed on the Washington-Pipelines github FAQ page listed a
>>FreesurferNHP pipeline
>>(https://github.com/Washington-University/Pipelines/wiki/FAQ#9-what-if-i-
>>want-to-process-non-human-primate-nhp-data-with-the-hcp-pipelines), but
>>it hasn't been released yet.
>> 
>> Do you know when this pipeline will be available? Alternatively, is
>>there another way I can obtain the pipeline scripts and template volumes?
>> 
>> Thank you,
>> Pete Lauro
>> 
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>> 
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Re: [Freesurfer] T2 vs. T2-FLAIR update

[Matt Glasser]

And I would say if you want to do T1w/T2w myelin mapping the T2w scan will
give you more contrast for that, as the fluid inversion does seem to
reduce your contrast for myelin some (though it may increase your contrast
for CSF).  FLAIR can be useful for other things (like seeing some kinds of
brain lesions more easily) so your choice might depend on what else you
want to do with the images.

Peace,

Matt.

On 7/18/16, 6:59 PM, "Bruce Fischl"
 wrote:

>Hi Michelle
>
>that's a tough question. We don't have a ton of experience with it one
>way or the other, but if I had to pick one I would pick FLAIR as long as
>you are getting a 3D FLAIR with around 1mm voxels
>
>cheers
>Bruce
>On Mon, 18 Jul 2016,
>Michelle T Kassel wrote:
>
>> 
>> Hello, 
>> 
>> 
>> I am beginning a new study and would like to determine the
>> optimal T2 acquisition parameters for improved pial surface
>> results from FreeSurfer. I am wondering if there is a difference in
>>using a
>> T2 or T2-FLAIR. I have found a discussion post from 2014 which provided
>> useful 
>>information(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-J
>>uly/039580.ht
>> ml), however, it seems from reading the post that newer developments
>>were
>> underway, and I was wondering if I could get an updated answer to the
>> question:
>> 
>> 
>> is there any difference from freesurfer's perspective of using T2-space
>>or
>> T2-space-flair?
>> 
>> 
>> Thank you for your help!
>> 
>> 
>> Michelle
>> 
>> 
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Re: [Freesurfer] Support for surface data on NeuroVault.org

[Matt Glasser]

Hi Chris,

Why not focus on distributing GIFTI files that are viewable both by
FreeSurfer and many other applications instead of FreeSurfer¹s native
format?  For the same reason that it is helpful to provide NIFTI files
because of their strong, cross-platform adoption, it would be more helpful
to provide GIFTI files in your database so that a wider range of users could
use them without converting them.  You could probably automatically convert
FreeSurfer¹s native formats to GIFTI with FreeSurfer¹s utility mris_convert
on upload if you didn¹t want your uploading users to have to do the
conversions.  

Generally inflated surfaces are easiest for viewing patterns, but it is
often helpful to include anatomical surfaces as well.

Peace,

Matt.

From:   on behalf of Chris Filo
Gorgolewski 
Reply-To:  Freesurfer support list 
Date:  Saturday, August 20, 2016 at 12:21 PM
To:  freesurfer 
Subject:  [Freesurfer] Support for surface data on NeuroVault.org

Dear FreeSurfer community,
I am one of the developers of NeuroVault.org   - an
open repository for vizualizing, analyzing, and sharing of statistical and
parcellation maps of the human brain. So far NeuroVault was limited only to
volumetric data in the MNI space since this is the most common way of
reporting MRI results. Now I would like to start working on adding support
for surface data beginning with outputs of FreeSurfer. Since I'm not a
FreeSurfer expert I would like to ask the community a few questions:

1. In NeuroVault users are asked to upload their statistical maps in form of
files. I'm planning to target outputs of mri_glmfit: preferably Z.mgh but
also sig.mgh. Is this the most sensible thing to do?

2. I want to be able to tell if a given map is in fsaverage space. Is there
any place in the .mgh header that specifies which space the map is in?

3. fsaverage has different subsampling flavours - how often are they used?
Is support for them an important feature?

4. Results come in two files - one per each hemisphere. Is there any way
(from the headers) to check if two files provided by a user match?

5. As with the volumetric data I want to provide a 3D interactive viewer. I
had some initial success with Brain Browser. Are you aware of any other
javascript based viewers that work well with FreeSurfer data?

6. Which surface should be the default view: inflated, pial, or white?

7. Finally NeuroVault gives users ability to compare maps and even search
through the whole repository to find statistical maps with similar patterns.
This is currently implemented for volumetric data, but could be extended to
surface data. The problem arises when one wants to compare MNI volumetric
data with fsaverage surface data. So far I have been using mri_vol2surf with
target subject being fsaverage (with a supplied affine correction matrix),
but this solution is far from optimal since fsaverage folding patterns are
quite different from MNI. I was thinking that maybe a more accurate way of
dealing with this would be to reconstruct MNI152 cortical surface model, do
surface registration of it to fsaverage, and use that to sample statistical
maps in MNI space. What do you think?

Thank you for any help feedback you can provide!

Best,
Chris Gorgolewski
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Re: [Freesurfer] Support for surface data on NeuroVault.org

[Matt Glasser]

GIFTI has two identical formats for scalar (e.g. Statistical) data.
.func.gii and .shape.gii are basically identical.  It is also a good idea to
provide some surfaces upon which to display the GIFTI data.

I¹m a bit puzzled as to how to display arbitrary scalar overlays at all in
FreeView (though I figured out how to display label/annot files which worked
fine as GIFTI).  I don¹t know anything about pysurfer.

Peace,

Matt.

From:   on behalf of Chris Filo
Gorgolewski 
Reply-To:  Freesurfer support list 
Date:  Saturday, August 20, 2016 at 1:51 PM
To:  Freesurfer support list 
Subject:  Re: [Freesurfer] Support for surface data on NeuroVault.org

On Sat, Aug 20, 2016 at 10:39 AM, Matt Glasser  wrote:
> Why not focus on distributing GIFTI files that are viewable both by FreeSurfer
> and many other applications instead of FreeSurfer¹s native format?  For the
> same reason that it is helpful to provide NIFTI files because of their strong,
> cross-platform adoption, it would be more helpful to provide GIFTI files in
> your database so that a wider range of users could use them without converting
> them.  You could probably automatically convert FreeSurfer¹s native formats to
> GIFTI with FreeSurfer¹s utility mris_convert on upload if you didn¹t want your
> uploading users to have to do the conversions.
I was merely discussing the format required for the upload - which I want to
keep as straightforward as possible for the users. As you mentioned we can
do a conversion server side and provide other file formats. Having an
optional download the data as gifti might be very useful. Would that be a
"Functional" gifti file? So .func.gii? This does not seem right since many
statistical maps will come from anatomical data. I cannot find the right
intent in the GIFTI spec (section 13): it's not a set of coordinates,
neither a label map... How are statistical maps usually stored in gifti?

Would we also need to provide each map in .mgh or is .gii sufficient for
FreeSurfer users? Is displaying statistical map overlay coming in a form of
a .gii file easy in FreeView? What about pysurfer?

> Generally inflated surfaces are easiest for viewing patterns, but it is often
> helpful to include anatomical surfaces as well.
Thanks!

Best,
Chris 
> 
> Peace,
> 
> Matt.
> 
> From:   on behalf of Chris Filo
> Gorgolewski 
> Reply-To:  Freesurfer support list 
> Date:  Saturday, August 20, 2016 at 12:21 PM
> To:  freesurfer 
> Subject:  [Freesurfer] Support for surface data on NeuroVault.org
> 
> Dear FreeSurfer community,
> I am one of the developers of NeuroVault.org <http://NeuroVault.org>  - an
> open repository for vizualizing, analyzing, and sharing of statistical and
> parcellation maps of the human brain. So far NeuroVault was limited only to
> volumetric data in the MNI space since this is the most common way of
> reporting MRI results. Now I would like to start working on adding support for
> surface data beginning with outputs of FreeSurfer. Since I'm not a FreeSurfer
> expert I would like to ask the community a few questions:
> 
> 1. In NeuroVault users are asked to upload their statistical maps in form of
> files. I'm planning to target outputs of mri_glmfit: preferably Z.mgh but also
> sig.mgh. Is this the most sensible thing to do?
> 
> 2. I want to be able to tell if a given map is in fsaverage space. Is there
> any place in the .mgh header that specifies which space the map is in?
> 
> 3. fsaverage has different subsampling flavours - how often are they used? Is
> support for them an important feature?
> 
> 4. Results come in two files - one per each hemisphere. Is there any way (from
> the headers) to check if two files provided by a user match?
> 
> 5. As with the volumetric data I want to provide a 3D interactive viewer. I
> had some initial success with Brain Browser. Are you aware of any other
> javascript based viewers that work well with FreeSurfer data?
> 
> 6. Which surface should be the default view: inflated, pial, or white?
> 
> 7. Finally NeuroVault gives users ability to compare maps and even search
> through the whole repository to find statistical maps with similar patterns.
> This is currently implemented for volumetric data, but could be extended to
> surface data. The problem arises when one wants to compare MNI volumetric data
> with fsaverage surface data. So far I have been using mri_vol2surf with target
> subject being fsaverage (with a supplied affine correction matrix), but this
> solution is far from optimal since fsaverage folding patterns are quite
> different from MNI. I was thinking that maybe a more accurate way of dealing
> with this would be to reconstruct MNI152 cortical surface model, do surface
> registration of it to fsaverage, and use that to sample statistic

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

[Matt Glasser]

PALM handles GIFTI and CIFTI data.

Peace,

Matt.

On 8/29/16, 6:21 PM, "Douglas N Greve"
 wrote:

>Does PALM do surface-based? Also, there is no way to appropriately
>handle this. For permutation, non-orthogonal designs are wrong. There
>are ways to try to compensate for it, which is what PALM is doing. Sorry
>to be nit-picky!
>
>
>On 08/29/2016 06:12 PM, Harms, Michael wrote:
>> Hi Maaike,
>> Why not just use PALM?  Then you don¹t have to worry about this (since
>> PALM appropriately handles the situation of correlated covariates).
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>>
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave.Tel: 314-747-6173
>> St. Louis, MO  63110Email: mha...@wustl.edu
>>
>>
>>
>>
>> On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>of
>> Douglas N Greve" > gr...@nmr.mgh.harvard.edu> wrote:
>>
>> It is hard to say. Since the subjects are not exchangeable, the
>> permutation is technically not appropriate. Check the winkler paper,  I
>> think he talks about what happens if you just don't do anything.
>>
>>
>> On 08/29/2016 11:07 AM, maaike rive wrote:
>>> Hi all,
>>>
>>>
>>> Is using forced permutation for non-orthogonal design matrices wrong
>>> or is it allowed to do this instead of using tools like palm (what
>>> happens eg with the covariates when using forced permutation)? I
>>> used forced permutation  and it seemed to work, results were (partly)
>>> comparable to what I found with monte carlo simulations.
>>>
>>>
>>> Thanks, Maaike
>>>
>>> 
>>>
>>> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu
>>>  namens Harms, Michael
>>> 
>>> *Verzonden:* vrijdag 26 augustus 2016 01:00:13
>>> *Aan:* Freesurfer support list
>>> *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing
>>> running after 3 days!
>>>
>>> Hi,
>>> You might want to check out FSL¹s PALM tool, which has a bit more
>>> sophisticated permutation framework, and allows for permutation in the
>>> context of non-orthogonal covariates.
>>>
>>> cheers,
>>> -MH
>>>
>>> --
>>> Michael Harms, Ph.D.
>>> ---
>>> Conte Center for the Neuroscience of Mental Disorders
>>> Washington University School of Medicine
>>> Department of Psychiatry, Box 8134
>>> 660 South Euclid Ave.Tel: 314-747-6173
>>> St. Louis, MO  63110Email: mha...@wustl.edu
>>>
>>> From: >> > on behalf of Ajay
>>> Kurani mailto:dr.ajay.kur...@gmail.com>>
>>> Reply-To: Freesurfer support list >> >
>>> Date: Thursday, August 25, 2016 at 4:13 PM
>>> To: Freesurfer support list >> >
>>> Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running
>>> after 3 days!
>>>
>>> Hi Doug,
>>> Thanks for the help!  I think I figured out the issue based on your
>>> response.
>>> 1) I created a template to use for this group and named it fsaverage
>>> (including creating monte carlo simulations) for simplicity of
>>> integrating with freesurfer as I am newer to it.  This is why the
>>> sizes didn't match up as you expected
>>>  but the mri_glmfit still ran.
>>>
>>> 2) I deleted the folder and restarted without background processes.
>>> The error became apparent.  Of my covariates (2 fix factors and 3
>>> quantitative), not all were orthogonal.  In looking at the error more,
>>> it seems that i need to add the
>>> --perm-force if I wanted the simulation to run, however the background
>>> processes were not aware of this error and kept polling as you
>>>mentioned.
>>>
>>> This brings me to a new but related issue.  From what I have read in
>>> other freesurfer posts, it is statistically incorrect to use
>>> --perm-force for non-orthogonal covariates (or continuous covariates).
>>> I am unsure how to proceed.
>>> a) If I ran permutation testing (to overcome the issue of incorrect
>>> smoothness estimations from the gaussian distribution assumption),
>>> then I run into the issue of non-orthogonal covariates.  Is there a
>>> way to orthogonalize the data in
>>>  freesurfer, or a solution to this issue?
>>>
>>> b) If orthogonalizing is difficult to implement, another option is
>>> running Qdec with the montecarlo simulation at a more conservative p
>>> value (p< 0.001).  From your previous posts, the testing at this p
>>> value for 10mm seems to meet the 5% FPR.  One question is if the
>>> non-orthogonal data affects this analysis as well for this model?
>>>
>>> Thanks,
>>> Ajay
>>>
>>> On Thu, Aug 25, 2016 at 12:18 PM, Ajay Kurani
>>> mailto:dr.ajay.kur...@gmail.com>> wrote:
>>>
>>>  Hi Freesurfer Experts,
>>> I am trying to use freesurfer's mri_glmfit-sim tool to run
>>>  permutation tes

Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Matt Glasser]

Sure there¹s a publication.  See Figure 14:

http://www.sciencedirect.com/science/article/pii/S1053811913005053

Peace,

Matt.

On 8/30/16, 10:21 AM, "Bruce Fischl"
 wrote:

>Hi Don
>
>the T2 or FLAIR helps us avoid dura. It is still a beta version though as
>we don't have a ton of experience with it, and no, there is no reference
>for it yet (or maybe ever) :)
>Bruce
>
>
>On Tue, 30 Aug 2016, Krieger, Donald N. wrote:
>
>> 
>> Dear list:
>> 
>>  
>> 
>> What are the advantages of including a T2 scan when running recon-all
>>­all
>>  ?
>> 
>> Which results can it effect and to what extent?
>> 
>> And how sensitive is freesurfer to artifacts in the T2 scan?
>> 
>> Is there a good reference for this/
>> 
>>  
>> 
>> Thanks and best - Don
>> 
>>  
>> 
>> 
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>contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Optimal combination of MRI-sequences

[Matt Glasser]

What do you mean by ³combining² sequences?

Peace,

Matt.

From:   on behalf of Erik Lindberg

Reply-To:  Freesurfer support list 
Date:  Tuesday, October 18, 2016 at 2:52 PM
To:  
Subject:  [Freesurfer] Optimal combination of MRI-sequences

Dear Freesufer experts,
 
We are in the process of starting a large MRI project on normal aging and
dementia.
 
There has been a lot of discussions about what sequences to use.
 
We are now thinking about combining several sequences. Is there an optimal
combination of MRI sequences for Freesufer?
 
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Re: [Freesurfer] freesufer v6 beta - T2 pial refinement performance and nsigma_below setting

[Matt Glasser]

How does it work if you just use vanilla recon-all v6 beta with the T2
refinement flag and the hires option?  We haven¹t yet updated the HCP
scripts for FreeSurfer v6, but this is on our to do list.

Peace,

Matt.

From:   on behalf of Antonin Skoch

Reply-To:  Freesurfer support list 
Date:  Sunday, November 27, 2016 at 7:03 PM
To:  
Subject:  [Freesurfer] freesufer v6 beta - T2 pial refinement performance
and nsigma_below setting

Dear FreeSurfer experts,

I have processed a group of subjects by the freesurfer v6 beta version
(with recent upgrade of mris_make_surfaces from 2016/11/21).

It seems to me that in contrast to v5.3 version (with the same nsigma_above
2, nsigma_below 3) the T2 pial refinement cuts out too much gray matter in
regions where the gray matter has rather low intensity in T2 images. I have
observed this behavior quite often in my subjects.

I have uploaded the example subject cut_gm_T2pial.tar.gz to the server. The
problematic area has RAS location 3.9, -70, 0. Also see the screenshot.

My command line was:

mris_make_surfaces -nsigma_above 2 -nsigma_below 3 -aseg aseg.hires -filled
filled.hires -wm wm.hires -mgz -sdir $my_subject_dir -orig white.deformed
-nowhite -orig_white white.deformed -orig_pial pial.preT2.pass2 -T2
my_subject/mri/T2w_hires.norm -T1 T1w_hires.norm -output .postT2.pass2
my_subject rh

and for FS 5.3

mris_make_surfaces -nsigma_above 2 -nsigma_below 3 -aseg aseg.hires -filled
filled.hires -wm wm.hires -mgz -sdir $my_subject_dir -orig white.deformed
-nowhite -orig_white white.deformed -orig_pial pial.preT2.pass2 -T2
my_subject/mri/T2w_hires.norm -T1 T1w_hires.norm -output
.postT2.pass2.FS_5.3 my_subject rh

Could you please comment on how to proceed?

It seems that in contrast to v5.3 it is necessary to increase nsigma_below
value since the nsigma values seem to be more "sensitive" in v6beta version.
I tried to increase nsigma_below (nsigma_below for T2 in recon-all is 5) but
it seemed to me that it leads to "leak" of the pial surface out of the gray
matter in other areas, mainly in regions adjacent to cerebellum. See the
example leaking the pial surface to the cerebellum in left hemisphere with
nsigma_below 5 in the second screenshot in attachment ( I have uploaded this
subject as file cut_gm_T2pial2.tar.gz, his cut-out gray matter RAS location
is -33.7, -18, 45, command line is similar as above, but for left
hemisphere). Yellow surface is with nsigma_below 5, blue is nsigma_below 3.
Btw, the -aseg option in mris_make_surfaces does not prevent to leak
surfaces into the cerebellum?

Could also be the reason of these problems, that I used HCP scripts which do
not do the T2 normalization with anatomy-informed mri_normalize (using aseg
and white surface), but only global normalization and bias field correction?

Regards,

Antonin Skoch
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Re: [Freesurfer] freesufer v6 beta - T2 pial refinement performance and nsigma_below setting

[Matt Glasser]

Hi Antonin,

In our experience with FreeSurfer 5.3 we were getting very consistent
results.  We are going to try some of this locally and work with the
FreeSurfer folks to get the T2w stream working robustly in FreeSurfer v6.0+.

Thanks for testing this,

Matt.

From:   on behalf of Antonin Skoch

Reply-To:  Freesurfer support list 
Date:  Wednesday, November 30, 2016 at 3:31 PM
To:  
Subject:  Re: [Freesurfer] freesufer v6 beta - T2 pial refinement
performance and nsigma_below setting

Dear experts,

given sub-optimal results of my surfaces I referred to in my previous post,
I have tested several different settings and input data preparation to
obtain optimal pial surfaces in my modified HCP pipeline. I tested all
variants in 5 representative subjects.

My modified HCP pipeline uses FreeSurfer V6beta and full hires recon (-cm
option) with 0.7mm3 data (including FreeSurferHiResWhite.sh and
FreeSurferHiResPial.sh where effectively no up and downsampling is done
since all steps are done in original 0.7 mm3 resolution).

I have played with input data and parameters of 2nd pass mris_make_surfaces
-T2pial in FreeSurferHiResPial.sh
Since FreeSurferHiResPial.sh does not use aseg-informed and white
surface-informed normalization and brain masking of T2 (which is default in
recon-all), I also tested performance of this option (using commands
borrowed from recon-all -T2pial). Since -nsigma_below 3 (default in
FreeSurferHiResPial.sh) with combination of freeSurfer V6beta version of
mris_make_surfaces cuts out some portions of gray matter in my data (in
contrast to FreeSurfer 5.3 version where it seems that nsigma_below 3
suffices!), I increased -nsigma_below to 5 (which is default value used in
recon-all -T2pial).

My tested versions were following:
For modified full hires HCP pipeline with FreeSurfer V6beta:
1. -nsigma_below 3 (original FreeSurferHiResPial.sh)
2. -nsigma_below 5 
3. -nsigma_below 5 with additional masking of T2 by brainmask.mgz
4. -nsigma_below 5 with aseg-informed normalization of T2 (using
mri_normalize)
5. -nsigma_below 5 with aseg-informed normalization of T2 (using
mri_normalize) and masking of T2 by brainmask.mgz

And, as Matt suggested, I also tried:
6. standard FreeSurfer V6 beta recon-all -pial and -T2pial (apart from
standard recon-all I used as ?h.white input the output of
FreeSurferHiResWhite.sh , but I think it should not matter in this context).

My observations are following:

It is definitely needed to increase -nsigma_below from 3 due to significant
cut out of portions of gray matter in some regions, in some subjects these
regions are very large.

Increase nsigma_below to 5 prevents cutting out of gray matter, however it
leads to leak of surfaces to cerebellum (as I showed in my previous post)
for all my versions (to varying extent). I am not sure how much significant
the extend of error is, looking subjective it seems significant, but
accounting the fact that the data is of high resolution, the maximal error
would be approx. 2 mm.

-nsigma_below 5 with aseg-informed normalization does not work well in some
areas and results in cutting out gray matter in some regions (but not to
such great extend as in nsigma_below 3)

FreeSurfer V6beta tends in some (not very large) areas to cut out gray
matter. On the other hand, in some areas and in some subjects it produces
largest leak of surfaces to dura and cerebellum from all my tested versions.

mri_normalize of T2 has in some regions  sub-optimal performance on pial
surface estimation and actually performs worse than global (no aseg-informed
and no white surface-informed) normalization ( especially at temporal poles,
but also in some areas at convexity).

I have indecisive results with masking. In some subjects it had almost no
effect, in one subject it definitely improved the leak to dura, but in some
subjects the results were quite opposite. I am not sure why the masking
should matter since the mask is larger than the regions where the surfaces
are extending, but I am not very familiar with internals of
mris_make_surfaces (the masked T2 maybe after internal smoothing in
mris_make_surfaces can propagate the voxel values even to regions relevant
for surface estimation). Therefore I would tend to use the masking.

Overall best results (better than with V6beta recon-all) I obtained with
-nsigma_below 5 with global (no aseg-informed and white surface-informed)
normalization of T2 as it is done in FreeSurferHiResPial.sh.

My overall impresion: I was quite frustrated to observe, how much the
results are dependent on particular setting of the parameters and input
data. But maybe my expectations of accuracy of surfaces were unrealistically
high

Regards,

Antonin
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Re: [Freesurfer] Major problems with T2-based pial removal

[Matt Glasser]

Also, what kind of T2w sequence is this?  I think we've mostly tested it
with the T2-SPACE (unless Bruce has tested with other things).

Peace,

Matt.

On 9/27/13 12:58 PM, "Bruce Fischl"  wrote:

>Hi Michael
>
>that looks pretty bad! What is the resolution of the T2? The T1 that you
>overlay on also looks somewhat blurry - what was it?
>
>Bruce
>
>
>On Fri, 27 Sep 
>2013, Michael Waskom wrote:
>
>> Hi, just to make the problem a bit more transparent, I took a second
>> screenshot of the slices with the pial surface from the -T2pial run in
>>red
>> and the pial surface from the normal run in
>> cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png
>> 
>> On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom 
>> wrote:
>>   Hi,
>> I'm using FS 5.3 and trying to use hires T2-weighted scans to refine
>> the pial mesh.
>> 
>> However, I've found that using the T2 is causing rather dramatic
>> problems with the pial surface.
>> 
>> I processed the same subject's data with and without the -T2pial
>> option. Here are links to a) pial surface image b) slices through the
>> volume and c) the recon-all.log:
>> 
>> With -T2pial
>> 
>> https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png
>> https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png
>> https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt
>> 
>> Without -T2pial
>> 
>> https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png
>> https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png
>> https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt
>> 
>> The release notes for 5.3 claim that the T2 is registered to the T1
>> before refining the surface, but I actually can't find any evidence of
>> that sequence in the log file. For this subject, the T1 and T2 came
>> from different scan sessions, although I have other data where they
>> were acquired in the same session that have similar, if less dramatic,
>> problems with the pial surface.
>> 
>> Any ideas?
>> 
>> Michael
>> 
>> 
>> 
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Re: [Freesurfer] Major problems with T2-based pial removal

[Matt Glasser]

Someone sent me a different kind of T2w image and it didn't work so well,
so we need to know what kind of image this is.

Peace,

Matt.

On 9/27/13 1:33 PM, "Bruce Fischl"  wrote:

>nope, pretty much only with T2-space with and without a flair pulse
>On Fri, 
>27 Sep 2013, Matt Glasser wrote:
>
>> Also, what kind of T2w sequence is this?  I think we've mostly tested it
>> with the T2-SPACE (unless Bruce has tested with other things).
>>
>> Peace,
>>
>> Matt.
>>
>> On 9/27/13 12:58 PM, "Bruce Fischl"  wrote:
>>
>>> Hi Michael
>>>
>>> that looks pretty bad! What is the resolution of the T2? The T1 that
>>>you
>>> overlay on also looks somewhat blurry - what was it?
>>>
>>> Bruce
>>>
>>>
>>> On Fri, 27 Sep
>>> 2013, Michael Waskom wrote:
>>>
>>>> Hi, just to make the problem a bit more transparent, I took a second
>>>> screenshot of the slices with the pial surface from the -T2pial run in
>>>> red
>>>> and the pial surface from the normal run in
>>>> cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png
>>>>
>>>> On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom
>>>>
>>>> wrote:
>>>>   Hi,
>>>> I'm using FS 5.3 and trying to use hires T2-weighted scans to refine
>>>> the pial mesh.
>>>>
>>>> However, I've found that using the T2 is causing rather dramatic
>>>> problems with the pial surface.
>>>>
>>>> I processed the same subject's data with and without the -T2pial
>>>> option. Here are links to a) pial surface image b) slices through the
>>>> volume and c) the recon-all.log:
>>>>
>>>> With -T2pial
>>>> 
>>>> https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png
>>>> https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png
>>>> https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt
>>>>
>>>> Without -T2pial
>>>> 
>>>> https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png
>>>> https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png
>>>> https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt
>>>>
>>>> The release notes for 5.3 claim that the T2 is registered to the T1
>>>> before refining the surface, but I actually can't find any evidence of
>>>> that sequence in the log file. For this subject, the T1 and T2 came
>>>> from different scan sessions, although I have other data where they
>>>> were acquired in the same session that have similar, if less dramatic,
>>>> problems with the pial surface.
>>>>
>>>> Any ideas?
>>>>
>>>> Michael
>>>>
>>>>
>>>>
>>>> ___
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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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>>>in
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>>> properly
>>> dispose of the e-mail.
>>
>>
>>
>>


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Re: [Freesurfer] Major problems with T2-based pial removal

[Matt Glasser]

So the T2-SPACE is a variable flip angle sequence that actually has a fair
amount of T1 and MT contrast in it and relatively less T2 contrast.  As a
result, you can clearly see the difference between grey and white matter,
and CSF is not massively brighter than grey and white matter.  If you are
using a different kind of T2w sequence where the distance between CSF
intensity and grey matter intensity is much greater, some of the internal
settings to the -T2pial flag will likely not be optimal.  I don't know if
recon-all allows you to modify those with expert options or not.  Bruce, is
it possible for the user to modify the ­nsigma_above and -nsigma_below flags
for mris_make_surfaces when using -T2pial?

Peace,

Matt.

From:  Michael Waskom 
Date:  Friday, September 27, 2013 2:20 PM
To:  Matt Glasser 
Cc:  Bruce Fischl ,
"Freesurfer@nmr.mgh.harvard.edu" 
Subject:  Re: [Freesurfer] Major problems with T2-based pial removal

Hi Matt,

It's this sequence:
http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2)

You can click the console screenshots for a closer view of the parameters --
let me know if you need me to track down more info.

mw


On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser  wrote:
> Someone sent me a different kind of T2w image and it didn't work so well,
> so we need to know what kind of image this is.
> 
> Peace,
> 
> Matt.
> 
> On 9/27/13 1:33 PM, "Bruce Fischl"  wrote:
> 
>> >nope, pretty much only with T2-space with and without a flair pulse
>> >On Fri,
>> >27 Sep 2013, Matt Glasser wrote:
>> >
>>> >> Also, what kind of T2w sequence is this?  I think we've mostly tested it
>>> >> with the T2-SPACE (unless Bruce has tested with other things).
>>> >>
>>> >> Peace,
>>> >>
>>> >> Matt.
>>> >>
>>> >> On 9/27/13 12:58 PM, "Bruce Fischl"  wrote:
>>> >>
>>>> >>> Hi Michael
>>>> >>>
>>>> >>> that looks pretty bad! What is the resolution of the T2? The T1 that
>>>> >>>you
>>>> >>> overlay on also looks somewhat blurry - what was it?
>>>> >>>
>>>> >>> Bruce
>>>> >>>
>>>> >>>
>>>> >>> On Fri, 27 Sep
>>>> >>> 2013, Michael Waskom wrote:
>>>> >>>
>>>>> >>>> Hi, just to make the problem a bit more transparent, I took a second
>>>>> >>>> screenshot of the slices with the pial surface from the -T2pial run
in
>>>>> >>>> red
>>>>> >>>> and the pial surface from the normal run in
>>>>> >>>> cyan: 
>>>>> https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png
>>>>> >>>>
>>>>> >>>> On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom
>>>>> >>>>
>>>>> >>>> wrote:
>>>>> >>>>   Hi,
>>>>> >>>> I'm using FS 5.3 and trying to use hires T2-weighted scans to refine
>>>>> >>>> the pial mesh.
>>>>> >>>>
>>>>> >>>> However, I've found that using the T2 is causing rather dramatic
>>>>> >>>> problems with the pial surface.
>>>>> >>>>
>>>>> >>>> I processed the same subject's data with and without the -T2pial
>>>>> >>>> option. Here are links to a) pial surface image b) slices through the
>>>>> >>>> volume and c) the recon-all.log:
>>>>> >>>>
>>>>> >>>> With -T2pial
>>>>> >>>> 
>>>>> >>>> https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png
>>>>> >>>> https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png
>>>>> >>>> https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt
>>>>> >>>>
>>>>> >>>> Without -T2pial
>>>>> >>>> 
>>>>> >>>> https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png
>>>>> >>>> https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png
>>>>> >>>> https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt
>>>>> >>>>
>>>>> >&

Re: [Freesurfer] Major problems with T2-based pial removal

[Matt Glasser]

I'm sure it was registered to the T1w with BBR, though I don't know the
internals of that in recon-all.  Given that you might only be the second
person to try this with non T2-SPACE T2w images (and I unfortunately had not
told Bruce about my bad experience with this), you can forgive the
FreeSurfer docs for not mentioning it yet. :)

That being said, it isn't guaranteed not to work, you just might have to do
some fiddling with the nsigma parameters to get it to work, as the defaults
for T2-SPACE are probably not good for your images.

Peace,

Matt.

From:  Michael Waskom 
Date:  Friday, September 27, 2013 10:06 PM
To:  Matt Glasser 
Cc:  Bruce Fischl ,
"Freesurfer@nmr.mgh.harvard.edu" 
Subject:  Re: [Freesurfer] Major problems with T2-based pial removal

Hmm, Ok. Thanks Matt.

I still think it's weird that the T2 didn't seem to ever get registered to
the FS volume, but it's not a huge loss if we can't use them. With that
said, it might help to clarify the docs on this point a bit, as it sort of
sounded like any reasonably-sized T2-weighted image would be useful, and I
would have tried to collect a different image if I had known!


On Fri, Sep 27, 2013 at 12:58 PM, Matt Glasser  wrote:
> So the T2-SPACE is a variable flip angle sequence that actually has a fair
> amount of T1 and MT contrast in it and relatively less T2 contrast.  As a
> result, you can clearly see the difference between grey and white matter, and
> CSF is not massively brighter than grey and white matter.  If you are using a
> different kind of T2w sequence where the distance between CSF intensity and
> grey matter intensity is much greater, some of the internal settings to the
> -T2pial flag will likely not be optimal.  I don't know if recon-all allows you
> to modify those with expert options or not.  Bruce, is it possible for the
> user to modify the ­nsigma_above and -nsigma_below flags for
> mris_make_surfaces when using -T2pial?
> 
> Peace,
> 
> Matt.
> 
> From:  Michael Waskom 
> Date:  Friday, September 27, 2013 2:20 PM
> To:  Matt Glasser 
> Cc:  Bruce Fischl ,
> "Freesurfer@nmr.mgh.harvard.edu" 
> Subject:  Re: [Freesurfer] Major problems with T2-based pial removal
> 
> Hi Matt,
> 
> It's this sequence:
> http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2)
> 
> You can click the console screenshots for a closer view of the parameters --
> let me know if you need me to track down more info.
> 
> mw
> 
> 
> On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser  wrote:
>> Someone sent me a different kind of T2w image and it didn't work so well,
>> so we need to know what kind of image this is.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> On 9/27/13 1:33 PM, "Bruce Fischl"  wrote:
>> 
>>> >nope, pretty much only with T2-space with and without a flair pulse
>>> >On Fri,
>>> >27 Sep 2013, Matt Glasser wrote:
>>> >
>>>> >> Also, what kind of T2w sequence is this?  I think we've mostly tested it
>>>> >> with the T2-SPACE (unless Bruce has tested with other things).
>>>> >>
>>>> >> Peace,
>>>> >>
>>>> >> Matt.
>>>> >>
>>>> >> On 9/27/13 12:58 PM, "Bruce Fischl"  wrote:
>>>> >>
>>>>> >>> Hi Michael
>>>>> >>>
>>>>> >>> that looks pretty bad! What is the resolution of the T2? The T1 that
>>>>> >>>you
>>>>> >>> overlay on also looks somewhat blurry - what was it?
>>>>> >>>
>>>>> >>> Bruce
>>>>> >>>
>>>>> >>>
>>>>> >>> On Fri, 27 Sep
>>>>> >>> 2013, Michael Waskom wrote:
>>>>> >>>
>>>>>> >>>> Hi, just to make the problem a bit more transparent, I took a second
>>>>>> >>>> screenshot of the slices with the pial surface from the -T2pial run
in
>>>>>> >>>> red
>>>>>> >>>> and the pial surface from the normal run in
>>>>>> >>>> cyan: 
>>>>>> https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png
>>>>>> >>>>
>>>>>> >>>> On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom
>>>>>> >>>>
>>>>>> >>>> wrote:
>>>>>> >>>>   Hi,
>>>>>> >>>> I'm using

Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)

[Matt Glasser]

I think the latest version of FSL has this sorted out (it doesn't change
your machine's POSIXLY_CORRECT setting except briefly in the middle of
fsl_sub).

Peace,

Matt.

From:  chenchunhuichina 
Date:  Friday, November 1, 2013 2:55 AM
To:  Matt Glasser 
Cc:  free surfer 
Subject:  ERROR: comparison in expression (FS with SGE)

Dear Matt and freesurfers,
 
I am encounting this old problem, that is, using fsl_sub to launch
FreeSurfer jobs in SGE and get this error message: (standard_in) 2: Error:
comparison in expression
and freesurfer stoped. But running freesurfer without fsl_sub is OK (using
fsl_sub to launch other commonds also fine).
 
Following Matt's message on this problem
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-May/023961.html,
I added a line "POSIXLY_CORRECT=0 " in fsl_sub under  the line "set --
`getopt T:q:a:p:M:j:t:z:N:Fvm:l:s: $*`"
which now looks like this
...
set -- `getopt T:q:a:p:M:j:t:z:N:Fvm:l:s: $*`
POSIXLY_CORRECT=0 
...
 
However, the error was still the same, and what's even worse is that seems
the job was launched twice.
 
So can Matt or anybody tell me why? Am I misunderstood Matt's message? or
mybe version differences since Matt's solution came out one year ago?
I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0, FMRIB Software
Library, Release 5.0 (c) 2012
 
there are two fsLsub
./src/sgeutils/fsl_sub
./bin/fsl_sub
which one should I edit or both?
 
Any help is appreciated, Thank you all!
 
 
2013-11-01 

Chunhui Chen
_
 
State Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China 100875


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Re: [Freesurfer] T2pial/FLAIRpial processing issues

[Matt Glasser]

To fix the second problem, why not reorient the T2w image so the image axes
are oriented in the way that FreeSurfer expects?

Peace,

Matt.

From:  Martijn Steenwijk 
Date:  Thursday, November 14, 2013 8:13 AM
To:  freesurfer 
Cc:  Veronica Popescu , Hugo Vrenken 
Subject:  [Freesurfer] T2pial/FLAIRpial processing issues

Dear all,

There seem to be some serious issues with the T2pial / FLAIRpial processing
options provided in the latest versions of FreeSurfer.

First of all, although not clearly documented, T2pial / FLAIRpial processing
does require the FSLDIR to be set (in order to use bbregister with
--init-fsl). If not set,  recon-all will finish just without using the T2 or
FLAIR information. Importantly, no clear warning about this is given
although the user expects that T2/FLAIR has been used for pial surface
refinement. I think this is a very easy source of errors, so it might be a
good idea to just throw an error when FSLDIR is missing and T2pial/FLAIRpial
processing is requested.

Second, if FSLDIR has been set. T2pial/FLAIRpial uses bbregister with FLIRT
initialisation to align the T2 or FLAIR image to orig.mgz. However, we have
some high-res 3DFLAIR data in which this registration (more specifially, the
FLIRT initialisation step of bbregister) seems to fail in more than half of
the cases. Apparently, the FSL initialisation is not capable to change the
orientation such that it fits to the coordinate system used for orig.mgz.
Again, no warning or error is thrown, but the processing just continues with
the wrong registration and without noticing the results will get worse
compared to not using T2 or FLAIR.
Although I know its essential to look at the output data; would it be
possible to put some effort in letting the user know that things got wrong?

As a sidenote; I tried to fix this registration issue, but it seems to be
very complicated using bbregister (other than just inserting my own
registration obtained by using FLIRT to register native FLAIR to native T1,
and subsequently transform the result to Freesurfer space in order to obtain
FLAIR.mgz). 

Best,
Martijn
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Re: [Freesurfer] T2pial/FLAIRpial processing issues

[Matt Glasser]

I think you can do it with mri_convert ­rl.  I don't think it makes sense to
expect FLIRT to get the registration right reliably if the axes are off (in
the HCP Pipelines we definitely don't expect this and make sure all images
are RPI before processing them).

Peace,

Matt.

From:  Martijn Steenwijk 
Date:  Thursday, November 14, 2013 9:27 AM
To:  Bruce Fischl 
Cc:  Veronica Popescu , Hugo Vrenken ,
freesurfer 
Subject:  Re: [Freesurfer] T2pial/FLAIRpial processing issues

Hi Matt, Bruce, 

The problems are indeed a flirt issue, but given that it's programmed with
--init-fsl there is not much flexibility.

However, from a FS point of view, it might be a better and more robust
approach to first register FLAIRraw.mgz to raw.mgz, and then concatenate the
resulting registration with the (header based) registration from raw.mgz to
orig.mgz - instead of trusting the robustness of either registration
algorithms. 

... or, as Matt suggests, fix the image axes appropriately after converting
the FLAIR to mgz, and then run the registration. But I'm not sure how to do
that.

Best,
Martijn  


On Thu, Nov 14, 2013 at 5:53 PM, Bruce Fischl 
wrote:
> Hi Martijn
> 
> we can print warning and errors if FSLDIR is not set, but the registration
> errros seem to be mostly a flirt issue, no? Have you posted on the FSL list?
> 
> Bruce
> 
> 
> On Thu, 14 Nov 2013, Martijn Steenwijk wrote:
> 
>> Dear all,
>> There seem to be some serious issues with the T2pial / FLAIRpial processing
>> options provided in the latest versions of FreeSurfer.
>> 
>> First of all, although not clearly documented, T2pial / FLAIRpial processing
>> does require the FSLDIR to be set (in order to use bbregister with
>> --init-fsl). If not set,  recon-all will finish just without using the T2 or
>> FLAIR information. Importantly, no clear warning about this is given
>> although the user expects that T2/FLAIR has been used for pial surface
>> refinement. I think this is a very easy source of errors, so it might be a
>> good idea to just throw an error when FSLDIR is missing and T2pial/FLAIRpial
>> processing is requested.
>> 
>> Second, if FSLDIR has been set. T2pial/FLAIRpial uses bbregister with FLIRT
>> initialisation to align the T2 or FLAIR image to orig.mgz. However, we have
>> some high-res 3DFLAIR data in which this registration (more specifially, the
>> FLIRT initialisation step of bbregister) seems to fail in more than half of
>> the cases. Apparently, the FSL initialisation is not capable to change the
>> orientation such that it fits to the coordinate system used for orig.mgz.
>> Again, no warning or error is thrown, but the processing just continues with
>> the wrong registration and without noticing the results will get worse
>> compared to not using T2 or FLAIR.
>> Although I know its essential to look at the output data; would it be
>> possible to put some effort in letting the user know that things got wrong?
>>  
>> 
>> As a sidenote; I tried to fix this registration issue, but it seems to be
>> very complicated using bbregister (other than just inserting my own
>> registration obtained by using FLIRT to register native FLAIR to native T1,
>> and subsequently transform the result to Freesurfer space in order to obtain
>> FLAIR.mgz). 
>> 
>> Best,
>> Martijn
>> 
>> 
> 
> 
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> 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
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Re: [Freesurfer] T2pial/FLAIRpial processing issues

[Matt Glasser]

So the T2w image is already having the axes realigned to RAS with
mri_convert in FreeSurfer prior to running -init-fsl?  If that is the
case, FLIRT should work well enough assuming the input orientation
information in the T2w and T1w NIFTI headers was accurate.  I suppose you
could also restrict the -searchxyz angles to +/-30 degrees to keep FLIRT
from making large (and incorrect if the axes are aligned) image rotations.

Peace,

Matt.

On 11/14/13 9:52 AM, "Bruce Fischl"  wrote:

>Hi Matt
>
>hopefully Doug will chime in, but I don't see why that is the case. We
>preserve all the RAS information when we "conform", so the info should be
>there for flirt
>
>cheers
>Bruce
>
>
>On Thu, 14 Nov 2013, Matt Glasser wrote:
>
>> I think you can do it with mri_convert ?rl.  I don't think it makes
>>sense to
>> expect FLIRT to get the registration right reliably if the axes are off
>>(in
>> the HCP Pipelines we definitely don't expect this and make sure all
>>images
>> are RPI before processing them).
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: Martijn Steenwijk 
>> Date: Thursday, November 14, 2013 9:27 AM
>> To: Bruce Fischl 
>> Cc: Veronica Popescu , Hugo Vrenken
>>,
>> freesurfer 
>> Subject: Re: [Freesurfer] T2pial/FLAIRpial processing issues
>> 
>> Hi Matt, Bruce, 
>> The problems are indeed a flirt issue, but given that it's programmed
>>with
>> --init-fsl there is not much flexibility.
>> 
>> However, from a FS point of view, it might be a better and more robust
>> approach to first register FLAIRraw.mgz to raw.mgz, and then
>>concatenate the
>> resulting registration with the (header based) registration from
>>raw.mgz to
>> orig.mgz - instead of trusting the robustness of either registration
>> algorithms. 
>> 
>> ... or, as Matt suggests, fix the image axes appropriately after
>>converting
>> the FLAIR to mgz, and then run the registration. But I'm not sure how
>>to do
>> that.
>> 
>> Best,
>> Martijn  
>> 
>> 
>> On Thu, Nov 14, 2013 at 5:53 PM, Bruce Fischl
>>
>> wrote:
>>   Hi Martijn
>>
>>   we can print warning and errors if FSLDIR is not set, but the
>>   registration errros seem to be mostly a flirt issue, no? Have
>>   you posted on the FSL list?
>>
>>   Bruce
>>
>>   On Thu, 14 Nov 2013, Martijn Steenwijk wrote:
>>
>> Dear all,
>> There seem to be some serious issues with the T2pial
>> / FLAIRpial processing
>> options provided in the latest versions of
>> FreeSurfer.
>>
>> First of all, although not clearly documented,
>> T2pial / FLAIRpial processing
>> does require the FSLDIR to be set (in order to use
>> bbregister with
>> --init-fsl). If not set,  recon-all will
>> finish just without using the T2 or
>> FLAIR information. Importantly, no clear warning
>> about this is given
>> although the user expects that T2/FLAIR has been
>> used for pial surface
>> refinement. I think this is a very easy source of
>> errors, so it might be a
>> good idea to just throw an error when FSLDIR is
>> missing and T2pial/FLAIRpial
>> processing is requested.
>>
>> Second, if FSLDIR has been set. T2pial/FLAIRpial
>> uses bbregister with FLIRT
>> initialisation to align the T2 or FLAIR image to
>> orig.mgz. However, we have
>> some high-res 3DFLAIR data in which this
>> registration (more specifially, the
>> FLIRT initialisation step of bbregister) seems to
>> fail in more than half of
>> the cases. Apparently, the FSL initialisation is not
>> capable to change the
>> orientation such that it fits to the coordinate
>> system used for orig.mgz.
>> Again, no warning or error is thrown, but the
>> processing just continues with
>> the wrong registration and without noticing the
>> results will get worse
>> compared to not using T2 or FLAIR.
>> Although I know its essential to look at the output
>> data; would it be
>> possible to put some effort in letting the user kn

Re: [Freesurfer] Occipital cortex segmentation

[Matt Glasser]

Higher than 1mm resolution helps a lot.  We use 0.7mm isotropic in the HCP.

Peace,

Matt.

From:  "Megha K." 
Date:  Monday, December 9, 2013 10:23 PM
To:  
Subject:  [Freesurfer] Occipital cortex segmentation

Dear Sir/Madam,

I am using freesurfer for 3T MRI analysis of visual cortical thickness in
elderly patients with ophthalmic disease. We are having a bit of trouble
with the accuracy of cortical segmentation in the visual cortex (namely the
pericalcarine region) as the cortex is quite thin in our patients (compared
to controls). You can see in the attached image that whilst there is smooth
cortical segmentation in the peri-calcarine region, the cortex is not
visible to the naked eye.  If you have any ideas on improving accuracy, I
would be very grateful.

Thanks
Megha
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Re: [Freesurfer] Time taken by Freesurfer for processing

[Matt Glasser]

Newer versions also have the ability to run some stages on multiple CPU
cores (with the -openmp  flag) which speeds certain stages (e.g. in
autorecon2) up considerably.  I'm also sure Bruce wouldn't turn down more
resources to hire the programmers needed to make it faster either!

Peace,

Matt.

On 1/23/14 11:25 AM, "Bruce Fischl"  wrote:

>Hi Tanya
>we have always preferenced minimizing manual interactions over computer
>time. It takes so long because of its level of automation and its
>completeness. This is also why it is so widely used I assume - because it
>generates a comprehensive, accurate and automated morphometric assay of
>the 
>human brain. Seems like waiting a few extra hours to get something
>complete, automated and accurate isn't a big deal.
>
>cheers
>
>Bruce
>
>On Thu, 
>23 Jan 2014, Tanya Verma wrote:
>
>> Hi,
>> I would like to ask that why does the Freesurfer takes so much time for
>> processing particularly autorecon2 ?
>> 
>> Knowing that Freesurfer takes a lot of time for processing, why is it
>>still
>> used widely by researchers ? For segmentation followed by volume
>>calculation
>> , does one has to really wait for hours for the results?
>> 
>> Thank you
>> 
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Re: [Freesurfer] poor grey/white distinction in superior part of scan

[Matt Glasser]

Some pictures would probably be helpful to know what the issue is.

Peace,

Matt.

From:  Christine Smith 
Date:  Thursday, January 23, 2014 1:05 PM
To:  
Subject:  [Freesurfer] poor grey/white distinction in superior part of scan

Hello,

I am emailing to inquire about whether poor grey/white contrast in one part
of a scan (i.e., the posterior and superior part of the scan; ~parietal
cortex) can be addressed. The contrast in other parts of the scan looks good
and freesurfer does a great job of distinguishing white from grey. For the
parietal cortex area the cortex appears very thin. In addition, the entire
brain appears 'white' or bright, even though the brain doesn't look this
bright if you reconstruct it from dicoms.

We have now obtained 4 scans like this, so it isn't just one person with
thinning cortex. 

How can I make an adjustment to only this superior part of the brain and
leave the rest of it alone? Or do I need to make an adjustment to the
intensity early on for the entire scan and then basically start over with
editing? 

Best,
Christine

-- 
Christine N. Smith, Ph.D.
Department of Psychiatry
University of California, San Diego
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[Freesurfer] FW: poor grey/white distinction in superior part of scan

[Matt Glasser]

From:  Christine Smith 
Date:  Thursday, January 23, 2014 3:58 PM
To:  Matt Glasser 
Subject:  Re: [Freesurfer] poor grey/white distinction in superior part of
scan

Please note that the left and right sides of the brain are flipped for
freesurfer vs the dicom picture. Please find attached a dicom picture that
is oriented the same way as freesurfer. Sorry for any confusion.


On Thu, Jan 23, 2014 at 1:56 PM, Christine Smith  wrote:
> Dear Matt, 
> 
> Please find attached two pictures. One is of the brain from reconstructed
> dicom files (using AFNI). The other one is a pic from tkmedit of the same
> subject and approximately the same slice of brain. Notice that the freesurfer
> image is very bright. Look at the white matter and pial lines (i.e., cortical
> thickness) in the upper left hand part of the image and see how thin the
> cortex appears. Notice also, that there is very little grey/white contrast in
> this same area in the brain image reconstructed from dicoms.
> 
> Please let me know if there are any other pictures you might desire or
> information you might need.
> 
> Christine
> 
> 
> On Thu, Jan 23, 2014 at 11:33 AM, Matt Glasser  wrote:
>> Some pictures would probably be helpful to know what the issue is.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From:  Christine Smith 
>> Date:  Thursday, January 23, 2014 1:05 PM
>> To:  
>> Subject:  [Freesurfer] poor grey/white distinction in superior part of scan
>> 
>> Hello,
>> 
>> I am emailing to inquire about whether poor grey/white contrast in one part
>> of a scan (i.e., the posterior and superior part of the scan; ~parietal
>> cortex) can be addressed. The contrast in other parts of the scan looks good
>> and freesurfer does a great job of distinguishing white from grey. For the
>> parietal cortex area the cortex appears very thin. In addition, the entire
>> brain appears 'white' or bright, even though the brain doesn't look this
>> bright if you reconstruct it from dicoms.
>> 
>> We have now obtained 4 scans like this, so it isn't just one person with
>> thinning cortex.
>> 
>> How can I make an adjustment to only this superior part of the brain and
>> leave the rest of it alone? Or do I need to make an adjustment to the
>> intensity early on for the entire scan and then basically start over with
>> editing? 
>> 
>> Best,
>> Christine
>> 
>> -- 
>> Christine N. Smith, Ph.D.
>> Department of Psychiatry
>> University of California, San Diego
>> ___ Freesurfer mailing list
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>> was sent to you in error but does not contain patient information, please
>> contact the sender and properly dispose of the e-mail.
> 
> 
> 
> -- 
> Christine N. Smith, Ph.D.
> Department of Psychiatry
> University of California, San Diego



-- 
Christine N. Smith, Ph.D.
Department of Psychiatry
University of California, San Diego


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Re: [Freesurfer] using multiple cores

[Matt Glasser]

If you are compiling with clang openmp might not work.

Peace,

Matt.

On 5/2/14, 2:13 PM, "Bruce Fischl"  wrote:

>Hi Lukas
>
>sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going
>on? 
>Does OpenMP have to be enabled somehow?
>
>Bruce
>
>
>On Fri, 2 May 2014,
>lukas.sch...@ukb.uni-bonn.de wrote:
>
>> Hi Bruce!
>> 
>> I just run: recon-all -s ernie2  -autorecon2 -openmp 4
>> 
>> mri_ca_register  uses 100.9% CPU at most ...
>> 
>> Any idea?  Should I try to recompile FS for the current MacOS release?
>>If
>> so, do I have to take care on special librariwa in order to enable the
>> openmp option?
>> 
>> Best wishes,
>> 
>> Lukas
>> 
>> >Hi Bruce!
>> >
>> >Thanks for the fast response. I used the current stable version 5.3.0.1
>> >(freesurfer-Darwin-lion-stable-pub-v5.3.0.1).
>> >So I will try as you have suggested ...
>> >
>> >Best wishes,
>> >
>> >Lukas
>> 
>> >> Bruce Fischl Fri, 02 May 2014 05:47:26 -0700
>> >>
>> >> Hi Luke
>> >>
>> >> what version of FS are you running? We see significant speedups. Try
>> >> running top in a unix terminal and seeing if the cpu usage of
>> >> mri_ca_register (during autorecon2, the longest single step) is
>>morethan
>> >>100%
>> >>
>> >> cheers
>> >> Bruce
>> >>
>> >> On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote:
>> >>
>> >>
>> >> > Hi folks!
>> > > >
>> >> > I try to use -openmp option on an iMAC with 4 cores.
>>Unfortunately, I
>> > >>do not
>> >> > see any accelartion when processing a single data set with or
>>without
>> > >>the
>> >> > flag -openmp flag set.
>> >> >
>> >> > recon-all -s ernie_1 -all
>> >> >
>> >> > leads to ~6,4h processing time.
>> >> >
>> >> > Unfortunately
>> >> > recon-all -s ernie_2 -all -openmp 4
>> >> >
>> >> > did not change anything. Do I miss anything? Do I have to prepare
>>my
>> > >>system
>> >> > in a special way? Or run any scripts in advance?
>> >> >
>> >> > (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS
>> >> >version)
>> >> >
>> >> > Best wishes,
>> >> >
>> >> > Luke
>> 
>> 
>> 
>> 
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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

[Matt Glasser]

Hi Bruce,

For whatever reason, sometimes the T2w surface adjustment will be way off.
Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit up and
down can get it out of the minimum and make it work, so there might be a
bug.  

Peace,

Matt.

From:  "Emil H.J. Nijhuis" 
Reply-To:  Freesurfer support list 
Date:  Friday, May 9, 2014 at 4:53 AM
To:  
Subject:  Re: [Freesurfer] problem with pial surface reconstruction using T1
(MPRAGE) and T2 (SPACE) weighted images

Dear Bruce,

thank you for your help.

attached I have put an fslview, tkmedit screen-shot of the T2 image and a
tksurfer image of lh.woT2.pial.

It appears that without consideration of the T2 this effect does not happen.

What would be your recommendation if I would like to keep using the T2
weighted image?

Yours,

 Emil



Hi Emil

how do the surfaces look before you apply the T2 deformation? And how do
they look visualized over the T2 instead of the T1?
cheers
Bruce

On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
> Hi,
> 
> I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm
> isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio
> scanner with a 32-channel head coil. Unfortunately for half of my subjects I
> receive an rather odd pial surface artefact, while the 'white' surfaces do
> not suffer from the same issue.
> 
> The command line I have used was:
> 
> recon-all -all -subjid  -T2  /mri/orig/T2.mgz -T2pial
> -3T
> 
> Are you familiar with this issue and do you have some advice for me?
> 
> Thank you very much for your help.
> 
> Yours sincerely,
> 
>  Emil
> 
> --
> --
> Emil H.J. Nijhuis, PhD
> Researcher - Division of Diagnostic and Interventional Neuroradiology
> University Hospital Basel
> Petersgraben 4
> CH 4031 Basel Switzerland
> 
> 
> 
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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

[Matt Glasser]

Probably Emil¹s current example would be best because it is failing in
your recon-all setup.

Matt.

On 5/9/14, 9:31 AM, "Bruce Fischl"  wrote:

>Hi Matt
>
>if you can send me an example I'll try to find time to take a look
>Bruce
>On Fri, 9 
>May 2014, Matt Glasser wrote:
>
>> Hi Bruce,
>> 
>> For whatever reason, sometimes the T2w surface adjustment will be way
>>off.
>>  Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit up
>>and
>> down can get it out of the minimum and make it work, so there might be a
>> bug.  
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: "Emil H.J. Nijhuis" 
>> Reply-To: Freesurfer support list 
>> Date: Friday, May 9, 2014 at 4:53 AM
>> To: 
>> Subject: Re: [Freesurfer] problem with pial surface reconstruction
>>using T1
>> (MPRAGE) and T2 (SPACE) weighted images
>> 
>> Dear Bruce,
>> 
>> thank you for your help.
>> 
>> attached I have put an fslview, tkmedit screen-shot of the T2 image and
>>a tk
>> surfer image of lh.woT2.pial.
>> 
>> It appears that without consideration of the T2 this effect does not
>>happen.
>> 
>> What would be your recommendation if I would like to keep using the T2
>>weigh
>> ted image?
>> 
>> Yours,
>>  Emil
>> 
>> Hi Emil
>> 
>> how do the surfaces look before you apply the T2 deformation? And how do
>> they look visualized over the T2 instead of the T1?
>> 
>> cheers
>> Bruce
>> 
>> On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
>> 
>> Hi,
>> 
>> I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm
>> isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T
>>Trio
>> scanner with a 32-channel head coil. Unfortunately for half of my
>>subjects I
>> receive an rather odd pial surface artefact, while the 'white' surfaces
>>do
>> not suffer from the same issue.
>> 
>> The command line I have used was:
>> 
>> recon-all -all -subjid  -T2  /mri/orig/T2.mgz
>>-T2pial
>> -3T
>> 
>> Are you familiar with this issue and do you have some advice for me?
>> 
>> Thank you very much for your help.
>> 
>> Yours sincerely,
>> 
>>  Emil
>> 
>> --
>> --
>> Emil H.J. Nijhuis, PhD
>> Researcher - Division of Diagnostic and Interventional Neuroradiology
>> University Hospital Basel
>> Petersgraben 4
>> CH 4031 Basel Switzerland
>> 
>> 
>> 
>> ___
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>>sti
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Re: [Freesurfer] MPRAGE SNR

[Matt Glasser]

There is also the issue that grey and white matter are not truly a
homogeneous single intensity anatomically.

Peace,

Matt.

On 10/19/15, 9:23 AM, "Harms, Michael"

wrote:

>
>Hi,
>
>FWIW, I've looked at a number of these measures in 500+ subjects from HCP
>data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
>relate to each other, and whether they correlate with mean cortical
>thickness, white matter surface area, or number of SurfaceHoles (prior to
>topology correction).
>
>I didn't find much of note.  e.g., the highest correlations were:
>
>r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
>r = -0.25 between white surface area and wmanatsnr
>r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
>norm.mgz)
>
>Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
>0.49).
>
>G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
>G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97
>
>In another context (but smaller number of subjects), I've looked to see if
>these various snr, cnr measures from FS were related to manual quality
>ratings, and the relationship was rather weak.
>
>All-in-all, I haven't seen much that would indicate that these measures
>can be used as a sort of "automated" QC measure.  Manual review of the
>structurals and FS results is still needed.
>
>That said, the structurals from the HCP 500 release were all of reasonably
>good quality to begin with.  So, it is possible that these snr/cnr
>measures might be more informative in identifying truly awful scans in a
>clinical population with a wider variability in MPRAGE scan quality.
>
>I'd certainly be interested in hearing from anyone if they have found that
>to be the case in their data.
>
>BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from
>orig.mgz and norm.mgz respectively.
>Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively.
>
>cheers,
>-MH
>
>--
>Michael Harms, Ph.D.
>
>---
>Conte Center for the Neuroscience of Mental Disorders
>Washington University School of Medicine
>Department of Psychiatry, Box 8134
>660 South Euclid Ave.Tel: 314-747-6173
>St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
>On 10/19/15 8:09 AM, "Bruce Fischl"  wrote:
>
>probably similar, although maybe Doug can comment. You probably want to
>run
>it on the orig.mgz as the intensity normalization can artificially
>increase
>the SNR (which is kind of the point)
>Bruce
>
>
>On Mon, 19 Oct 2015, John
>Anderson wrote:
>
>> Hi Bruce,
>> Thanks a lot!! this is really great!
>> I ran the command as the following :
>>
>> mri_cnr subj_01/surf subj_01/mri/norm.mgz
>> processing MRI volume subj_01/mri/norm.mgz...
>> white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5
>> gray/white CNR = 2.291, gray/csf CNR = 0.848
>> lh CNR = 1.569
>> white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0
>> gray/white CNR = 2.278, gray/csf CNR = 0.798
>> rh CNR = 1.538
>> total CNR = 1.554
>>
>>
>> I noticed that the normal range for the SNR  (15-20) when using the
>>command
>> "wm-anat-snr"
>>
>> What is the normal range for cnr generated by the binary "mri_cnr"?
>>
>>
>> Bests,
>> John Anderson
>>
>> Senior Research Associate
>> Psychological and Brain Sciences Dept.
>> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
>> Phone: +1 (603) 646-9834
>> Fax: +1 (603) 646-1419
>> Sent: Monday, October 19, 2015 at 8:36 AM
>> From: "Bruce Fischl" 
>> To: "Freesurfer support list" 
>> Cc: j.haen...@psychologie.uzh.ch
>> Subject: Re: [Freesurfer] MPRAGE SNR
>> Hi John
>>
>> there is also a binary called mri_cnr that will compute the
>> contrast-to-noise ratio (CNR), which is really the more interesting
>> metric. It will also spit out the WM means+- std, and the ratio of these
>> two can be used as an SNR measure.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 19 Oct 2015, John Anderson wrote:
>>
>> > Dear Jürgen
>> > This really helps!
>> > I highly appreciate your input on this.
>> >
>> > Bests,
>> > John Anderson
>> >
>> > Senior Research Associate
>> > Psychological and Brain Sciences Dept.
>> > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
>> > Phone: +1 (603) 646-9834
>> > Fax: +1 (603) 646-1419
>> > Sent: Monday, October 19, 2015 at 1:30 AM
>> > From: JuergenHaenggi 
>> > To: "Freesurfer support list" 
>> > Subject: Re: [Freesurfer] MPRAGE SNR
>> > Dear John
>> > FS's QA tools provide the SNR
>> > see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools
>> >
>> > there is also a FS function called wm-anat-snr that can be used for
>>that.
>> >
>> > Hope this helps
>> > Cheers
>> > Jürgen
>> >
>>
>>>
>>>-
>>>--
>>
>> > --
>> > Jürgen Hänggi, Ph.D.
>> > Division of Neuropsychology
>> > Institute of Psychology
>> > University of Zurich
>> > Binzmuehlestr

Re: [Freesurfer] T2pial shrinks pial surface

[Matt Glasser]

What FreeSurfer version are you using?  Very small changes to the input
images (e.g. a different random see for FreeSurfer) may be able to kick
mris_make_surfaces out of that bug, though perhaps Bruce has fixed it.

Peace,

Matt.

From:   on behalf of Chris Adamson

Reply-To:  Freesurfer support list 
Date:  Sunday, March 6, 2016 at 6:14 PM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] T2pial shrinks pial surface

The T2pial option mostly works beautifully. I have a few cases where the
pial surface just shrinks globally and wraps over the white surface (see
attached). I have checked the T2.mgz and the registration with the T1 is
fine. This happens sometimes in one hemisphere only.
Any ideas?
 
Chris Adamson
Senior Research Officer
Developmental Imaging
Murdoch Childrens Research Institute
The Royal Children¹s Hospital
Flemington Rd Parkville, Victoria 3052 AUS
T: (03) 9936 6780
E: chris.adam...@mcri.edu.au
www.mcri.edu.au 
 
 




 
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Re: [Freesurfer] Surface based analysis using FA maps

[Matt Glasser]

I too am puzzled as to why you would want to do this.  In terms of getting
improvement in the alignment across subjects TBSS is one way to approach
this.  Another would be to use the fiber orientations in the registration
like these folks have done:
http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage

If you are interested in studying the properties of cortical grey matter
there might be better modalities than FA.  If you can provide more details
on what you are trying to do, perhaps that would clarify how to go about
it?

Peace,

Matt.

On 3/22/16, 2:49 PM, "Douglas N Greve"
 wrote:

>I don't know of a reference where someone has done this (though I would
>be surprised if it is not out there), so just be aware of this if you
>try to publish. The commands look correct, however, you may or may not
>want to sample in the middle of the cortical ribbon (--projfrac 0.5).
>Since this is a DTI analysis, wouldn't you want to sample in the WM?
>Doing that is a little tricky, but you can use something like --projabs
>-1 to sample 1mm *away* from the ribbon into the WM.
>
>On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:
>>
>> Dear FS experts,
>>
>> I would like to run surface based analysis using FA maps. I am not
>> exactly sure that what I am doing is totally right specially step 2 .
>> I used the following commands:
>>
>> 1.I registered the FA maps to T1 using the command:  bbregister --s
>> bert --mov dtifit_FA.nii --bold --init-fsl --reg  reg.dat
>>
>> 2.I concatenated the subject¹s FA maps using the command :
>>  mris_preproc ­target fsaverage ­hemi lh ­iv .bert1/dtifit_FA.nii
>> reg.dat ­iv bert2/dtifit_FA.nii reg.dat Š. --projfrac 0.5 --out
>>lh.FA.mgz
>>
>> 3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5
>> --cortex --sval  lh.FA.mgz --tval lh.FA_5mm.mgz
>>
>> 4.Then GLM analysis using mri_glmfit
>>
>> 5.Correction for multiple comparison mri_glmfit-sim
>>
>> Kindly, are these steps correct? I used the previous steps to do
>> surface based analysis using PET images and it worked very well. While
>> for the FA maps it seems that there is something wrong and I can¹t
>> figure out what it is!
>>
>> I highly appreciate any input on this!
>>
>> Best,
>>
>> Mohamad
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
>The information in this e-mail is intended only for the person to whom it
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>contains patient information, please contact the Partners Compliance
>HelpLine at
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Re: [Freesurfer] Surface based analysis using FA maps

[Matt Glasser]

Right but what do you think FA, MD, AD, RD, etc are telling you
neurobiologically in the grey matter?

Matt.

On 3/23/16, 7:18 PM, "Alshikho, Mohamad J."
 wrote:

>Hi Matt,
>I highly appreciate your input on this!!
>
>Actually my goal is to study the difference in FA values between groups
>within the cortex. I know that diffusivities ( MD, AD and RD) can be used
>to evaluate gray matter and many people claim that it is much better to
>use diffusivities to evaluate gray matter But my interest is specifically
>in FA within the gray matter.
>
>For that reason I want to do surface based analysis to study the
>differences in FA between my study groups. I checked for the optimal ways
>to do it: 
>1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
>2. And I found 
>https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028109
>.html
>
>I ran the analysis using both methods.
>
>For the second method I replaced PET maps by FA maps and this was the
>reason for my question! If we can do the analysis that way using PET
>maps, why we can't do it using FA maps?
>
>I will be more than happy if you can suggest me an alternative approach
>to study FA on a surface.
>
>
>Best,
>Mohamad
>
>-Original Message-
>From: freesurfer-boun...@nmr.mgh.harvard.edu
>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
>Sent: Wednesday, March 23, 2016 8:04 PM
>To: Freesurfer support list 
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>I too am puzzled as to why you would want to do this.  In terms of
>getting improvement in the alignment across subjects TBSS is one way to
>approach this.  Another would be to use the fiber orientations in the
>registration like these folks have done:
>http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage
>
>If you are interested in studying the properties of cortical grey matter
>there might be better modalities than FA.  If you can provide more
>details on what you are trying to do, perhaps that would clarify how to
>go about it?
>
>Peace,
>
>Matt.
>
>On 3/22/16, 2:49 PM, "Douglas N Greve"
>gr...@nmr.mgh.harvard.edu> wrote:
>
>>I don't know of a reference where someone has done this (though I would
>>be surprised if it is not out there), so just be aware of this if you
>>try to publish. The commands look correct, however, you may or may not
>>want to sample in the middle of the cortical ribbon (--projfrac 0.5).
>>Since this is a DTI analysis, wouldn't you want to sample in the WM?
>>Doing that is a little tricky, but you can use something like --projabs
>>-1 to sample 1mm *away* from the ribbon into the WM.
>>
>>On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:
>>>
>>> Dear FS experts,
>>>
>>> I would like to run surface based analysis using FA maps. I am not
>>> exactly sure that what I am doing is totally right specially step 2 .
>>> I used the following commands:
>>>
>>> 1.I registered the FA maps to T1 using the command:  bbregister --s
>>> bert --mov dtifit_FA.nii --bold --init-fsl --reg  reg.dat
>>>
>>> 2.I concatenated the subject¹s FA maps using the command :
>>>  mris_preproc ­target fsaverage ­hemi lh ­iv .bert1/dtifit_FA.nii
>>>reg.dat ­iv bert2/dtifit_FA.nii reg.dat Š. --projfrac 0.5 --out
>>>lh.FA.mgz
>>>
>>> 3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5
>>> --cortex --sval  lh.FA.mgz --tval lh.FA_5mm.mgz
>>>
>>> 4.Then GLM analysis using mri_glmfit
>>>
>>> 5.Correction for multiple comparison mri_glmfit-sim
>>>
>>> Kindly, are these steps correct? I used the previous steps to do
>>> surface based analysis using PET images and it worked very well.
>>> While for the FA maps it seems that there is something wrong and I
>>> can¹t figure out what it is!
>>>
>>> I highly appreciate any input on this!
>>>
>>> Best,
>>>
>>> Mohamad
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>--
>>Douglas N. Greve, Ph.D.
>>MGH-NMR Center
>>gr...@nmr.mgh.harvard.edu
>>Phone Number: 617-724-2358
>>Fax: 617-726-7422
>>
>>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>Outgoing:

Re: [Freesurfer] Surface based analysis using FA maps

[Matt Glasser]

FA or fractional anisotropy explains the fraction of the diffusion that is
along the long axis of the diffusion tensor.  In so far as the diffusion
tensor is an accurate model of the underlying structural architecture,
what you say might be true (e.g. in the small number of white matter
regions with only one main fiber orientation).  Most of white matter has
multiple fiber orientations and thus the diffusion tensor is not a great
model.  In grey matter, the principle orientation of processes is radial
to the surface (e.g. radial fibers, major dendrites), but there are are
also tangential processes (e.g. Bands of Baillarger).  To get a decrease
in FA, one could do a number of things:

1) Decrease the strength of radial diffusion
2) Increase the strength of tangential diffusion
3) Decrease the strength of both radial and tangential diffusion

Are you looking for a measure that shows tissue damage?

Matt.

On 3/23/16, 7:55 PM, "Alshikho, Mohamad J."
 wrote:

>It can explain one thing "tissue integrity"
>
>It will tell us neurobiologically exactly what can tell us in tissues
>other than the brain such as liver, lung, heart, joints,  etc
>
>Mohamad
>
>
>-Original Message-
>From: freesurfer-boun...@nmr.mgh.harvard.edu
>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
>Sent: Wednesday, March 23, 2016 8:49 PM
>To: Freesurfer support list 
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>Right but what do you think FA, MD, AD, RD, etc are telling you
>neurobiologically in the grey matter?
>
>Matt.
>
>On 3/23/16, 7:18 PM, "Alshikho, Mohamad J."
>malshi...@mgh.harvard.edu> wrote:
>
>>Hi Matt,
>>I highly appreciate your input on this!!
>>
>>Actually my goal is to study the difference in FA values between groups
>>within the cortex. I know that diffusivities ( MD, AD and RD) can be
>>used to evaluate gray matter and many people claim that it is much
>>better to use diffusivities to evaluate gray matter But my interest is
>>specifically in FA within the gray matter.
>>
>>For that reason I want to do surface based analysis to study the
>>differences in FA between my study groups. I checked for the optimal
>>ways to do it:
>>1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
>>2. And I found
>>https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028
>>109
>>.html
>>
>>I ran the analysis using both methods.
>>
>>For the second method I replaced PET maps by FA maps and this was the
>>reason for my question! If we can do the analysis that way using PET
>>maps, why we can't do it using FA maps?
>>
>>I will be more than happy if you can suggest me an alternative approach
>>to study FA on a surface.
>>
>>
>>Best,
>>Mohamad
>>
>>-Original Message-
>>From: freesurfer-boun...@nmr.mgh.harvard.edu
>>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt
>>Glasser
>>Sent: Wednesday, March 23, 2016 8:04 PM
>>To: Freesurfer support list 
>>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>>
>>I too am puzzled as to why you would want to do this.  In terms of
>>getting improvement in the alignment across subjects TBSS is one way to
>>approach this.  Another would be to use the fiber orientations in the
>>registration like these folks have done:
>>http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage
>>
>>If you are interested in studying the properties of cortical grey
>>matter there might be better modalities than FA.  If you can provide
>>more details on what you are trying to do, perhaps that would clarify
>>how to go about it?
>>
>>Peace,
>>
>>Matt.
>>
>>On 3/22/16, 2:49 PM, "Douglas N Greve"
>>>gr...@nmr.mgh.harvard.edu> wrote:
>>
>>>I don't know of a reference where someone has done this (though I
>>>would be surprised if it is not out there), so just be aware of this
>>>if you try to publish. The commands look correct, however, you may or
>>>may not want to sample in the middle of the cortical ribbon (--projfrac
>>>0.5).
>>>Since this is a DTI analysis, wouldn't you want to sample in the WM?
>>>Doing that is a little tricky, but you can use something like
>>>--projabs
>>>-1 to sample 1mm *away* from the ribbon into the WM.
>>>
>>>On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:
>>>>
>>>> Dear FS experts,
>>>>
>>>> I would like to run surface based analysis using FA maps. I am not
>>>&g

Re: [Freesurfer] Surface based analysis using FA maps

[Matt Glasser]

The point is that more than tissue damage will cause changes to FA.

Matt.

On 3/23/16, 9:17 PM, "Alshikho, Mohamad J."
 wrote:

>This is theoritically correct!
>If we do DTI to study the liver. How these measures can explain the
>tissue? It is not only white matter and gray matter!
>
>All DTI measures can explain how much space we have between the cells.
>More space means low FA and high RD. The opposit correct as well.
>Given that they share the same formula. If we accept RD as a marker for
>gray matter integrity. We should accept FA a marker for gray matter
>integrity.
>
>Yes I am looking for an optimal measure to evaluate tissue damage.
>
>Mohamad
>
>From: freesurfer-boun...@nmr.mgh.harvard.edu
>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Matt Glasser
>[m...@ma-tea.com]
>Sent: Wednesday, March 23, 2016 9:29 PM
>To: Freesurfer support list
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>FA or fractional anisotropy explains the fraction of the diffusion that is
>along the long axis of the diffusion tensor.  In so far as the diffusion
>tensor is an accurate model of the underlying structural architecture,
>what you say might be true (e.g. in the small number of white matter
>regions with only one main fiber orientation).  Most of white matter has
>multiple fiber orientations and thus the diffusion tensor is not a great
>model.  In grey matter, the principle orientation of processes is radial
>to the surface (e.g. radial fibers, major dendrites), but there are are
>also tangential processes (e.g. Bands of Baillarger).  To get a decrease
>in FA, one could do a number of things:
>
>1) Decrease the strength of radial diffusion
>2) Increase the strength of tangential diffusion
>3) Decrease the strength of both radial and tangential diffusion
>
>Are you looking for a measure that shows tissue damage?
>
>Matt.
>
>On 3/23/16, 7:55 PM, "Alshikho, Mohamad J."
>malshi...@mgh.harvard.edu> wrote:
>
>>It can explain one thing "tissue integrity"
>>
>>It will tell us neurobiologically exactly what can tell us in tissues
>>other than the brain such as liver, lung, heart, joints,  etc
>>
>>Mohamad
>>
>>
>>-Original Message-
>>From: freesurfer-boun...@nmr.mgh.harvard.edu
>>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
>>Sent: Wednesday, March 23, 2016 8:49 PM
>>To: Freesurfer support list 
>>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>>
>>Right but what do you think FA, MD, AD, RD, etc are telling you
>>neurobiologically in the grey matter?
>>
>>Matt.
>>
>>On 3/23/16, 7:18 PM, "Alshikho, Mohamad J."
>>>malshi...@mgh.harvard.edu> wrote:
>>
>>>Hi Matt,
>>>I highly appreciate your input on this!!
>>>
>>>Actually my goal is to study the difference in FA values between groups
>>>within the cortex. I know that diffusivities ( MD, AD and RD) can be
>>>used to evaluate gray matter and many people claim that it is much
>>>better to use diffusivities to evaluate gray matter But my interest is
>>>specifically in FA within the gray matter.
>>>
>>>For that reason I want to do surface based analysis to study the
>>>differences in FA between my study groups. I checked for the optimal
>>>ways to do it:
>>>1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
>>>2. And I found
>>>https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028
>>>109
>>>.html
>>>
>>>I ran the analysis using both methods.
>>>
>>>For the second method I replaced PET maps by FA maps and this was the
>>>reason for my question! If we can do the analysis that way using PET
>>>maps, why we can't do it using FA maps?
>>>
>>>I will be more than happy if you can suggest me an alternative approach
>>>to study FA on a surface.
>>>
>>>
>>>Best,
>>>Mohamad
>>>
>>>-Original Message-
>>>From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt
>>>Glasser
>>>Sent: Wednesday, March 23, 2016 8:04 PM
>>>To: Freesurfer support list 
>>>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>>>
>>>I too am puzzled as to why you would want to do this.  In terms of
>>>getting improvement in the alignment across subjects TBSS is one way to
>>>approach this.  Another would be t

Re: [Freesurfer] axial or sagittal?

[Matt Glasser]

I¹d add that SNR may also change if you don¹t acquire as much data axially
as you did sagittally.  Really it¹s better to acquire your 3D
T1w/T2w/FLAIR scans sagittally as this is most efficient.

Peace,

Matt.

On 4/8/16, 10:23 AM, "Bruce Fischl"
 wrote:

>Hi Gamaliel
>
>many things will change when you change the slice direction - amount of
>wrap, possibly your FOV, slab-selection profile if your protocol is
>slab-selective, and some types of distortion. These will all change the
>image which will change our results. Of course even if you don't change
>anything you won't get identical results if you scan twice, but our
>longitudinal stream is pretty reliable. Andre van der Kouwe has
>acquitisiton recommendations here:
>
>http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_p
>rotocols.pdf
>
>cheers
>Bruce
>
>On Fri, 8 Apr 2016, Gamaliel
>Huerta Urrea wrote:
>
>> 
>> 
>> 2016-04-08 12:09 GMT-03:00 Gamaliel Huerta Urrea
>>:
>>   Hello Freesurfers
>> I'm trying to do volumetric reconstruction, i already have done this
>> but. i wanted to see if for the same subject, with different
>> directions of slices i have the same result, and obviously i had
>> different results of volumetric measures. i have used the sequence
>> FSPGR T1 ponderation, with the same parameters for both data
>> acquisition; with voxel 1 mm3, but the direction is changed in both
>> studies axial and sagittal. Both studies are in *.dcm format, and i
>> used the next command for convert dicom to .mgz and after to apply
>> recon-all process:
>>
>>  1.
>>
>> mri_convert firstdicom.dcm 001.mgz
>> 
>> I would like to know why would i have this problem?
>> 
>> There is some specific slice direction for this kind of study which is
>> suitable ?
>> 
>> I'm interested in cerebellum volumetric information. I attached my
>> results for volumetry.
>> 
>> Cheers
>> 
>> --
>> Gamaliel Huerta
>> Ingeniero Civil Biomédico
>> HealthCare Analytics
>> Centro Interdisciplinario de Innovación en Salud
>> Universidad de Valparaíso
>> 
>> 
>> 
>> 
>> --
>> Gamaliel Huerta
>> Ingeniero Civil Biomédico
>> HealthCare Analytics
>> Centro Interdisciplinario de Innovación en Salud
>> Universidad de Valparaíso
>> 
>> 
>>___
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>
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>contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Incorporating (high resolution) T2- and FLAIR volumes

[Matt Glasser]

I find the T2w image works well for removing dura and blood vessels, but
I'm not sure FLAIR would work for T1w/T2w myelin mapping because of what
would happen to the ratio near the pial surface.

Instructions for T1w/T2w myelin mapping are available here:
http://brainvis.wustl.edu/wiki/index.php/Caret:MyelinMaps

One starts with FreeSurfer outputs.

Bruce: do you guys have an unsmoothed group average grey/white map?  We
could do a quick comparison on fsaverage if you guys were interested.

Peace,

Matt.

On 3/28/13 7:45 AM, "Bruce Fischl"  wrote:

>1a) You would do this after running recon-all on the T1-weighted image.
>It 
>will only adjust the surfaces, not the segmentation. Something like
>recon-all -T2pial 
>
>1b) this will work with either, but in my experience the FLAIR helps more
>to distinguish dura from gm
>
>2) Yes. The standard aseg will label them and we have some custom tools
>that are more accurate if you have other image contrasts. I don't think
>they are quite distributed yet, but perhaps Doug can comment.
>
>3) Sure, this isn't too hard.  David Salat has published using the
>gray/white ratio as an interesting biomarker and the techniques would be
>pretty similar. I think Matt mostly used FreeSurfer for his analysis, but
>perhaps he can comment on the particulars
>
>cheers
>Bruce
>
>
>On Thu, 28 Mar 2013, lukas.sch...@ukb.uni-bonn.de wrote:
>
>> 
>> Hi FreeSurfer experts!
>> 
>> We have isotropic T1/T2 and FLAIR volumes for a larger cohort.  It
>>would be
>> fine to use the T2 / FLAIR volumes to improve the segmentation and to
>> perform a couple additional analyses using FS. This leads to the
>>following
>> questions:
>> 
>> 1) How do I incorporate T2/Flair volumes into the recon all processing
>> stream?
>> 
>> a) Would it be like:  recon-all bert -all -T2 /luke/xyz/007-T2.nii ?
>> 
>> b) What is expected to get the better results regarding the pial
>>surface:
>> FLAIR or T2? (both are at 1x1x1mm)
>> 
>> 2) Is there any module in FS to detect white matter lesions?
>> 
>> 3) How can I perform myelin mapping using the ratio method (T1w/T2w)?
>>Or do
>> I have to switch to Caret?
>> 
>> Many thanks in advance for your help and advice!
>> 
>> Best wishes,
>> 
>> Luke
>> 
>> 
>>___
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>
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>contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Advice on integrating FSL\'s BET with recon-all

[Matt Glasser]

Those pipelines will hopefully be available publicly this summer.  The
relevant code is this though:

recon-all -i  -subjid $SubjectID -sd $SubjectDIR -motioncor
-talairach -nuintensitycor -normalization
mri_convert 
"$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz --conform
mri_em_register -mask "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz
"$SubjectDIR"/"$SubjectID"/mri/nu.mgz
$FREESURFER_HOME/average/RB_all_2008-03-26.gca
"$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta
mri_watershed -T1 -brain_atlas
$FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca
"$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta
"$SubjectDIR"/"$SubjectID"/mri/T1.mgz
"$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz
cp "$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz
"$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz
recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 ­autorecon3

Basically,  you make mri_em_register give a more accurate registration (this
is typically what fails when you get a bad brain extraction from FreeSurfer
in my experience), and then use FreeSurfer's own very nice brain extraction
algorithm with the better registration to get the final brain mask.

Peace,

Matt.

From:  
Date:  Sunday, April 28, 2013 4:21 AM
To:  
Subject:  Re: [Freesurfer] Advice on integrating FSL\'s BET with recon-all

Hi Matt!

Refering to an older mail from  06 Mar 2013  I would be also interested to
integrate BET-results for the initial registration step.  Using the -B
option in BET I get very robust results.

You recommend: "... using the BET extracted image instead of the image with
skull for the initial registration step, and then you can use mri_watershed
on the original image..."

How can this be implemented practically? Are the HCP protocols / pipelines
you mentioned later available for the research community?

Many thanks in advance,

Luke

Matt Glasser 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:
%22Matt+Glasser%22>  Wed, 06 Mar 2013 16:09:44 -0800
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:
20130306> 

I would check the mri_em_register registrations of the step that
immediately precedes mri_watershed (and produces
talairach_with_skull.lta).  We found that most of the variability and
failures occurred in this step, and mri_watershed itself is a very robust
brain extraction algorithm when it is given an accurate registration (my
experience with BET is that it is probably not the best tool for getting
very accurate brainmasks and sometimes takes away too much). I would
recommend using the BET extracted image instead of the image with skull
for the initial registration step, and then you can use mri_watershed on
the original image and get good results every time.  This is the type of
strategy we use in the HCP Pipelines (except we use something more robust
than BET for the initial mask).

Note that the "talairach" registration (done by the -talairach step with
the talairach_avi tool) has nothing to do with the registration that
precedes brain extraction.  Perhaps it should is more robust and should be
used, but the affine would have to be converted to the correct format.

Peace,

Matt.

On 3/6/13 3:53 PM, "Bruce Fischl"  wrote:

>you can use
>
>mri_convert -rl ...
>
>to reslice the output of bet so that it has the same geometry as the rest
>of our stream
>
>cheers
>Bruce
>
>On Wed, 6 Mar 2013, Winter, Warren wrote:
>
>> Hi again,
>> We have had some suboptimal results from FreeSurfer's skullstripping
>>algorithm, even after iteratively trying different
>> watershed thresholds and after checking the quality of Talairach
>>registration.  The results are pretty good, but often leave
>> some dura matter and bits of neck behind whose higher intensity values,
>>I believe, may end up skewing recon-all's later
>> estimation of the range of intensity values within grey matter, and
>>consequently compromising the accuracy of pial surface
>> estimation.
>> 
>> FSL's BET, however, seems to do a better job of extracting the brain,
>>at least for our dataset.  So, I was wondering if I
>> might be able to skip over mri_watershed and feed autorecon2 and
>>autorecon3 a brainmask.mgz file created using BET.  I tried
>> this procedure:
>> 
>> 
>> 1) mri_convert  T1.nii.gz
>> 2) bet T1.nii.gz BET_brainmask.nii.gz -A
>> 3) mri_convert BET_brainmask.nii.gz BET_brainmask.mgz
>> 4) recon-all -s  -autorecon1 -noskullstrip
>> 5) mv BET_brainmask.nii.gz .//mri/brainmask.mgz
>> 6) recon-all -s  -autorecon2 -autorecon3
>> 
&

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

[Matt Glasser]

This is available online now:

http://authors.elsevier.com/sd/article/S1053811913005053


On 5/7/13 3:10 PM, "Bruce Fischl"  wrote:

>actually Matt Glasser points out that a brief description is in his paper
>that is coming out soon, and there is also some description in Andre's
>multi-echo mprage paper
>Bruce
>On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
>wrote:
>
>> thanks :-)
>>
>> On May 7, 2013, at 3:28 PM, Bruce Fischl 
>>wrote:
>>
>>> no, of course not :)
>>>
>>> On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
>>> wrote:
>>>
>>>> Hi Bruce,
>>>>
>>>> Out of curiosity and for reference for my users, do you have a paper
>>>>on the T2 or FLAIR assisted segmentation?
>>>>
>>>> Cheers,
>>>> Souheil
>>>>
>>>> -
>>>>
>>>> Souheil Inati, PhD
>>>> Staff Scientist
>>>> FMRI Facility
>>>> NIMH/NIH/DHHS
>>>> souheil.in...@nih.gov<mailto:souheil.in...@nih.gov>
>>>>
>>>>
>>>>
>>>>
>>>> On May 7, 2013, at 2:24 PM, Bruce Fischl
>>>>mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>>>>
>>>> Hi Katie
>>>>
>>>> I'm really not sure. These days I would recommend a highres (e.g. 1mm
>>>> isotropic) FLAIR if you can get one, or T2 if not. The T2* can help,
>>>>but
>>>> it's pretty noisy in brain.
>>>>
>>>> cheers
>>>> Bruce
>>>>
>>>> On Tue, 7 May 2013, Katie Surrence wrote:
>>>>
>>>> Dear Freesurfer gurus,
>>>>
>>>> At the course, André van der Kouwe mentioned in his morphometry
>>>>methods talk that T2* weighted contrast from
>>>> MEMPRAGE could be used to further seperate dura from cortex, as also
>>>>discussed in this paper:
>>>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE
>>>>scanner in our lab.  The internet suggests
>>>> that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?
>>>>Would it work the same way?  Could you also
>>>> use these images with the mris_make_surfaces command?
>>>>
>>>> Thanks very much for your insight -- and I enjoyed the course!
>>>>
>>>> /Katie Surrence
>>>>
>>>> --
>>>> Research Coordinator
>>>> Social Cognition Laboratory
>>>> New York State Psychiatric Institute
>>>>
>>>> ___
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>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> 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] using T2* weighted scans to assist with dura stripping in a GE scanner?

[Matt Glasser]

Gordon Xu who helped us set up the protocol reminded me of the following:

"The main benefit of the readout PF is to reduce echo spacing, hence less
blurring in the slice direction. The side benefit is that it also reduces
the minimum TE, hence less dropout. However, you do give up some SNR at
the high spatial frequency as Souheil mentioned. There are two senarios of
this, a) the SNR is adequate, you only lose some SNR due to less sampling,
b) if the SNR is borderline or worse, in addition to losing SNR you also
lose some spatial resolution in the readout direction as the other side of
the high spatial frequency k-space is less reliable.

I remember we did pilot acquisition with and without "asymmetric echo" in
two subjects. You looked at the images and you either liked the one with
asymmetric echo because of less blurring or at least indifferent between
the two. So I assume with the Siemens 32ch coil we are in senario a)
above."


If I had to guess, we probably went with the readout partial fourier to
reduce the dropout regions in the gradient echo MPRAGE and didn't see an
obvious loss in resolution.

Peace,

Matt.

On 5/13/13 1:03 PM, "Inati, Souheil (NIH/NIMH) [E]"
 wrote:

>Hi Matt,
>
>Thanks for the link.
>
>Reading on pages 29-31, I am struck by the complexity of the procedure.
>Not to say that it doesn't work, or that the single T1w image free-surfer
>stuff is simple :-), on the contrary, it's just that I was expecting to
>see something about an optimization that used both images, rather than
>something based on the T1w image followed by an exclusion criterion based
>on the T2w image.  Anyway, works better than without.
>
>Minor question on the acquisition of the anatomicals:
>- Why are you using partial fourier in the read direction?  You're
>throwing away a lot of SNR at the high spatial frequencies, seems a shame
>to go to 0.7mm and then do that.
>
>Cheers,
>Souheil
>
>On May 12, 2013, at 10:54 PM, Matt Glasser  wrote:
>
>> This is available online now:
>> 
>> http://authors.elsevier.com/sd/article/S1053811913005053
>> 
>> 
>> On 5/7/13 3:10 PM, "Bruce Fischl"  wrote:
>> 
>>> actually Matt Glasser points out that a brief description is in his
>>>paper
>>> that is coming out soon, and there is also some description in Andre's
>>> multi-echo mprage paper
>>> Bruce
>>> On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
>>> wrote:
>>> 
>>>> thanks :-)
>>>> 
>>>> On May 7, 2013, at 3:28 PM, Bruce Fischl 
>>>> wrote:
>>>> 
>>>>> no, of course not :)
>>>>> 
>>>>> On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
>>>>> wrote:
>>>>> 
>>>>>> Hi Bruce,
>>>>>> 
>>>>>> Out of curiosity and for reference for my users, do you have a paper
>>>>>> on the T2 or FLAIR assisted segmentation?
>>>>>> 
>>>>>> Cheers,
>>>>>> Souheil
>>>>>> 
>>>>>> -
>>>>>> 
>>>>>> Souheil Inati, PhD
>>>>>> Staff Scientist
>>>>>> FMRI Facility
>>>>>> NIMH/NIH/DHHS
>>>>>> souheil.in...@nih.gov<mailto:souheil.in...@nih.gov>
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On May 7, 2013, at 2:24 PM, Bruce Fischl
>>>>>> mailto:fis...@nmr.mgh.harvard.edu>>
>>>>>>wrote:
>>>>>> 
>>>>>> Hi Katie
>>>>>> 
>>>>>> I'm really not sure. These days I would recommend a highres (e.g.
>>>>>>1mm
>>>>>> isotropic) FLAIR if you can get one, or T2 if not. The T2* can help,
>>>>>> but
>>>>>> it's pretty noisy in brain.
>>>>>> 
>>>>>> cheers
>>>>>> Bruce
>>>>>> 
>>>>>> On Tue, 7 May 2013, Katie Surrence wrote:
>>>>>> 
>>>>>> Dear Freesurfer gurus,
>>>>>> 
>>>>>> At the course, André van der Kouwe mentioned in his morphometry
>>>>>> methods talk that T2* weighted contrast from
>>>>>> MEMPRAGE could be used to further seperate dura from cortex, as also
>>>>>> discussed in this paper:
>>>>>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE
>>>>>> scanner in our 

Re: [Freesurfer] issue with pial surface in orbitofrontal cortex

[Matt Glasser]

Is the brain extraction removing that part of the brain?  Do you know
where the OFC ends and olfactory bulb begins?

Peace,

Matt.

On 5/16/13 11:43 AM, "Caspar M. Schwiedrzik"
 wrote:

>Hi!
>I am failing to get a proper pial surface in orbitofrontal cortex.
>See attached screenshot.
>This is NHP data, processed with version 4.5.
>I am not sure how to proceed here, as there is no clear with matter.
>Any advice would be appreciated.
>Thanks!
>Caspar
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Re: [Freesurfer] issue with pial surface in orbitofrontal cortex

[Matt Glasser]

Hard to fix if that is the receive field and you don't have another image
like a T2w to remove it with.  Perhaps mri_normalize can be tuned to
improve this with expert options as the white matter that is being
correctly segmented appears to be darker as well.

Peace,

Matt.

On 5/17/13 9:30 AM, "Bruce Fischl"  wrote:

>Hi Caspar
>
>yes, that might help. There are expert opts for this. Sorry, I have
>almost no experience analyzing monkey brains at .5mm, so I'm really not
>sure what to advise you. Perhaps one of the other people on list who have
>done a bunch can comment?
>Bruce
>On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
>
>> Hi Bruce,
>> I tried adding control points in the white matter in that region,
>> however, it does not seem to fix the issue. Also, the brainmask.mgz
>> does not seem to exclude this part of the brain, so that is not the
>> problem either.
>> I am attaching another screenshot (horizontal 119) to illustrate the
>>problem.
>> White matter pixel values range from the high 80ies to >100 in this
>>area.
>> Included grey matter pixel values are in the low 80ies.
>> Excluded grey matter pixel values range from the low 60ies to low 70ies.
>>
>> Would it make sense to re-run mri_segment with a different threshold?
>> Thanks, Caspar
>>
>>
>>
>> 2013/5/16 Bruce Fischl :
>>> Hi Caspar
>>>
>>> is the closest white matter captured by the white surface? What is the
>>> intensity of voxels there? If < 110 you could try putting control
>>>points in
>>> them and seeing if that helps (that is, in the closest voxels that are
>>> entirely white matter).
>>>
>>>
>>> Bruce
>>>
>>> On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote:
>>>
>>>> Hi Bruce,
>>>> ok.
>>>> But in theory, what would you recommend to get around the darkening
>>>> issue? Unfortunately, I do not have a field map available for this
>>>> data set.
>>>> Or should I not expect to get a pial surface in this area since the
>>>> white matter is not discernable?
>>>> There are five slices without clear white matter (original voxel size
>>>> 0.5x0.5x0.5 mm).
>>>> Thanks, Caspar
>>>>
>>>> 2013/5/16 Bruce Fischl :
>>>>>
>>>>> Hi Caspar
>>>>>
>>>>> if it's primate I don't think I'm going to be able to help - you'll
>>>>>need
>>>>> someone more familiar with primate anatomy
>>>>>
>>>>> sorry
>>>>> Bruce
>>>>> On Thu, 16 May 2013, Caspar M.
>>>>> Schwiedrzik wrote:
>>>>>
>>>>>> Hi Bruce and Matt,
>>>>>> yes, it is primate data. I just dropped an archive on your FTP
>>>>>>server
>>>>>> in transfer/incoming.
>>>>>> Thanks!
>>>>>> Caspar
>>>>>>
>>>>>> 2013/5/16 Matt Glasser :
>>>>>>>
>>>>>>> Is the brain extraction removing that part of the brain?  Do you
>>>>>>>know
>>>>>>> where the OFC ends and olfactory bulb begins?
>>>>>>>
>>>>>>> Peace,
>>>>>>>
>>>>>>> Matt.
>>>>>>>
>>>>>>> On 5/16/13 11:43 AM, "Caspar M. Schwiedrzik"
>>>>>>>  wrote:
>>>>>>>
>>>>>>>> Hi!
>>>>>>>> I am failing to get a proper pial surface in orbitofrontal cortex.
>>>>>>>> See attached screenshot.
>>>>>>>> This is NHP data, processed with version 4.5.
>>>>>>>> I am not sure how to proceed here, as there is no clear with
>>>>>>>>matter.
>>>>>>>> Any advice would be appreciated.
>>>>>>>> Thanks!
>>>>>>>> Caspar
>>>>>>>> ___
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>>>>>>>> e-mail
>>>>>>>> contains patient information, please contact the Partners
>>>>>>>>Compliance
>>>>>>>> HelpLine at
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>>>>>>>> but does not contain patient information, please contact the
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>>>>>>>> dispose of the e-mail.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
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>>>>
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Re: [Freesurfer] issue with pial surface in orbitofrontal cortex

[Matt Glasser]

Your line continuation isn't working for some reason?  Type the command
line all on one line and see if that fixes the problem.

Matt.

On 5/17/13 1:37 PM, "Caspar M. Schwiedrzik"
 wrote:

>set threshold = `echo "7/10" | bc -l`
>set segment_options = "-v -fillv -fillbg -wlo 104 -ghi 118  -whi 140
>-n 4 -p $threshold -keep"
>
>mri_segment ${segment_options} \
>-i brain.mgz -seg wm.mgz
>
>filling ventricles
>filling basal ganglia
>using white lolim = 104.0
>using gray hilim = 118.0
>using white hilim = 140.0
>running border classification 4 times
>preserving editing changes in output volume...
>using 70% threshold
>mri_read(): couldn't determine type of file
>mri_segment: could not read source volume from .700
>-i: Command not found
>
>
>2013/5/17 Bruce Fischl :
>> Hi Caspar
>>
>> can you include the command line and all the output?
>>
>>
>> Bruce
>> On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
>>
>>> filling ventricles
>>> filling basal ganglia
>>> using white lolim = 104.0
>>> using gray hilim = 118.0
>>> using white hilim = 140.0
>>> running border classification 4 times
>>> preserving editing changes in output volume...
>>> using 70% threshold
>>> mri_read(): couldn't determine type of file /.../.700
>>> mri_segment: could not read source volume from .700
>>> ../mri/brain.mgz: Permission denied
>>>
>>> if I add a -i to the input volume, it says flag not recognized.
>>> to get a floating point number into my tcsh script, I am using `echo
>>> "7/10" | bc -l`
>>>
>>> according to this previous discussion on the mailing list, there
>>> should be a fix available somewhere:
>>> 
>>>http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18824.html
>>>
>>> Thanks, Caspar
>>>
>>> 2013/5/17 Bruce Fischl :
>>>>
>>>> and what happens? Can you send the full screen output?
>>>>
>>>> On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
>>>>
>>>>> mri_segment \
>>>>> -v \
>>>>> -fillv \
>>>>> -fillbg \
>>>>> -wlo 104 \
>>>>> -ghi 118 \
>>>>> -whi 140 \
>>>>> -n 4 \
>>>>> -keep \
>>>>> brain.mgz wm.mgz
>>>>>
>>>>> The pial surface in the rest of the brain is ok, it is only the
>>>>> orbitofrontal/piriform cortex that is problematic. I now wanted to
>>>>>add
>>>>> -p 0.7.
>>>>>
>>>>> Caspar
>>>>>
>>>>>
>>>>> 2013/5/17 Bruce Fischl :
>>>>>>
>>>>>>
>>>>>> what is your command line? You are probably better off setting
>>>>>>gray_hi,
>>>>>> gray_low, wm_hi, wm_low, etc...
>>>>>>
>>>>>> Bruce
>>>>>> On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
>>>>>>
>>>>>>> When I try to specify a different threshold using -p, mri_segment
>>>>>>> reads in the threshold as the input volume.
>>>>>>> I tried specifying the input with -i (as explained here:
>>>>>>>
>>>>>>>
>>>>>>> 
>>>>>>>http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.
>>>>>>>html),
>>>>>>> but now it does not recognize the -i flag.
>>>>>>> Caspar
>>>>>>>
>>>>>>>
>>>>>>> 2013/5/17 Matt Glasser :
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Hard to fix if that is the receive field and you don't have
>>>>>>>>another
>>>>>>>> image
>>>>>>>> like a T2w to remove it with.  Perhaps mri_normalize can be tuned
>>>>>>>>to
>>>>>>>> improve this with expert options as the white matter that is being
>>>>>>>> correctly segmented appears to be darker as well.
>>>>>>>>
>>>>>>>> Peace,
>>>>>>>>
>>>>>>>> Matt.
>>>>>>>>
>>>>>>>> On 5/17/13 9:30 AM, "Bruce Fischl" 
>>&

[Freesurfer] FW: apply fnirt transformation on a surface

[Matt Glasser]

On 9/2/13 12:02 PM, "Glasser, Matthew"  wrote:

>Hi Bruce,
>
>Connectome Workbench commandline utilities can do this with FSL warp
>fields:
>
>wb_command -surface-apply-warpfield
>
>One needs to use the inverse warp as the  argument and the
>forward warp as the -fnirt .
>
>Peace,
>
>Matt.
>
>On 9/2/13 11:19 AM, "Bruce Fischl"  wrote:
>
>>A veritable game of telephone! Thanks Jesper. Matt?
>>
>>On Mon, 2 Sep 2013, Jesper Andersson wrote:
>>
>>> Hi guys,
>>> I didn't think we had any tools for doing that, and said so much on the
>>>FSL
>>> mailbase. But apparently the WashU people has something that does just
>>>that
>>> for you. I think the best person to contact about the details is Matt
>>> Glasser.
>>> 
>>> J
>>>  
>>> On 2 Sep 2013, at 15:58, Saad Jbabdi 
>>>  wrote:
>>>
>>>   Hi In Probtrackx, this is done internally.
>>> If you just want to transform the vertex coordinates, then I think
>>> you'll need to play with the FNIRT source code - I've CC'd Jesper who
>>> knows better.
>>> 
>>> Cheers,
>>> Saad
>>> 
>>> 
>>> 
>>> On 2 Sep 2013, at 15:56, Bruce Fischl 
>>> wrote:
>>>
>>>   you might check on the FSL list. I think I've seen some
>>>   traffic indicating that there are some tools for doing
>>>   this. I'l cc Saad as he might know
>>>
>>>   cheers
>>>   Bruce
>>> 
>>>
>>>   On Mon, 2 Sep 2013, Douglas Greve wrote:
>>>
>>> Hi Shani, I don't think you can apply a FNIRT
>>> transform to a surface.
>>> doug
>>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote:
>>>  Dear freesurfer people,
>>> Any idea whether I can apply transformation
>>> that was calculated by fsl
>>> fnirt on the white/pial surfaces calculated
>>> using the freesurfer
>>> stream?
>>> Thanks!
>>> Shani
>>> ___
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>>> 
>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
>>>
>>>   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.
>>> 
>>> 
>>> 
>>> --
>>> Saad Jbabdi
>>> University of Oxford, FMRIB Centre
>>> 
>>> JR Hospital, Headington, OX3 9DU, UK
>>> (+44)1865-222466  (fax 717)
>>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>>> 
>>> 
>>> 
>


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Re: [Freesurfer] version 2 FS

[Matt Glasser]

Note that this does not apply to HCP-style FreeSurfer runs or the HCP
released data.

Peace,

Matt.

On 9/7/13 8:26 AM, "Bruce Fischl"  wrote:

>Hi Anupa
>
>it means that for some acquisition types the pial surfaces in 5.2 had
>substantial errors. We recommend rerunning with 5.3. Note that this
>should 
>just involve compute time as all manual interventions will be retained
>
>cheers
>Bruce
>
>On 
>Sat, 7 Sep 2013, Anupa AV wrote:
>
>> Dear SIr,
>> 
>> I made some analysis based on FS v.2.0.
>> Does the Deprecated version means that the results generated by FSv.2
>>can't
>> be published???
>> 
>>
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Re: [Freesurfer] Ribbon

[Matt Glasser]

Hi Bruce,

He just needs the grey matter part of a typical ribbon.mgz volume.  He lost
some of his recon-all folder.  

Peace,

Matt.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Sunday, July 08, 2012 12:17 PM
To: Colin Reveley
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Ribbon

Hi Colin

what is the representation you want in the end? You can also fill the 
interior of the surfaces using mris_fill then do some boolean algebra on 
the results of e.g. the white and pial interiors.

cheers
Bruce


On Sun, 8 Jul 2012, Colin Reveley wrote:

> Hi - I need to make a ribbon volume. I have all the necessary surfaces,
but
> I'm lacking an aseg.mgz because the data is monkey. I saw one guy on the
> list had success by just calling his orig.mgz aseg.mgz. I tried that, and
it
> calculated the left right pial and white distances. Men sadly it
segfaulted.
> The program mri_ribbon will give me separate left and white gm ribbons. I
> combined those, coloured them 3 and 42 and did my level best to fill the
wm
> with the right values, but some bits are wrong.
> 
> What I'm actually trying to do is use matt glassers myelin mapping in
caret.
> other things could be wrong than my ribbon estimate.
> 
> If anyone has an idea how to make a good ribbon  without aseg I'd
appreciate
> it. Please bear in mind I may be missing much of what one gets when one
runs
> recon-all. I have thickness, curv, surfaces, filled.mgz, pretesselstion
> wm.mgz not so much else. The filled.mgz doesn't fill all non cortex the
way
> the bert ribbon does, so it's not that useful.
> 
> Thanks,
> 
> Colin
> 
>


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Re: [Freesurfer] (no subject)

[Matt Glasser]

What are the units of that measure?

 

Thanks,


Matt.

 

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Sunday, August 12, 2012 9:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] (no subject)

 

The values are in the ?h.sulc file
doug

On 8/12/12 10:12 PM, Hugh Pemberton wrote: 

Hi, 

 

How can I get sulcal depth measurements from Freesurfer? 

 

Cheers,

Hugh






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Re: [Freesurfer] bad acquisition and noise problem.

[Matt Glasser]

Are you using a 32-channel coil?  It looks like B1- receive field
inhomogeneity to me.

Peace,

Matt.

From:  youngmin huh 
Date:  Monday, November 12, 2012 10:22 PM
To:  Bruce Fischl ,

Subject:  Re: [Freesurfer] bad acquisition and noise problem.

Hi,
3D SPGR sequences were used. (TR=22, TE=4, thickness=1.4, FOV=240*240,
FA=40)
If the artifacts are due to B0 distortion, I wonder how I can fix it.

Thanks,
Youngmin Huh



2012/11/12 Bruce Fischl 
> Can you give us the acquisition details? I suspect this is not noise, but
> rather B0 distortion.
> what is the acquisition? And what bandwidth?
> 
> 
> On Nov 8, 2012, at 2:53 AM, youngmin huh  wrote:
> 
>> > Dear all,
>> >
>> > I'm working with some images, and they have so much noises on temporal
>> areas.
>> > I just ran recon2, but not sure if they'll be segmented properly.
>> > Does anyone have a recommendation for dealing with it?
>> > I wonder if there is any flag or option for this occasion.
>> > I would appreciate any comments or help.
>> > I attached an example.
>> >
>> > Thanks,
>> >
>> > Youngmin Huh
>> > 
> 
> 
> 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
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Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

[Matt Glasser]

If you get an MPRAGE and T2-SPACE you can make myelin maps too.
FreeSurfer's final surface placement benefits a lot from high resolution
images (less than 1mm) and you can still get good SNR with when you use
32-channel coils.  

Peace,

Matt.

On 11/20/12 4:41 PM, "Bruce Fischl"  wrote:

>Yes, definitely. The t2-space flair is a big help
>
>
>
>On Nov 20, 2012, at 5:40 PM, "Watson, Christopher"
> wrote:
>
>> Hi Bruce,
>> So would you recommend acquiring a T2 in addition to an
>>(ME)MPRAGE/SPGR? i.e. is it worth squeezing another acquisition into a
>>protocol?
>> 
>> Chris
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>>[fis...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, November 20, 2012 3:01 PM
>> To: Winter, Warren
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial
>>surface recons?
>> 
>> Hi Warren
>> 
>> yes, it will be part of the upcoming 5.2 release, hopefully in Dec. It
>> will use either a FLAIR or T2 (ideally T2-SPACE for either one)
>> 
>> cheers
>> Bruce
>> On Tue, 20
>> Nov 2012, Winter, Warren wrote:
>> 
>>> Hi all,
>>> 
>>> Back in January and October Bruce mentioned that he had under
>>>development some scripts designed to utilize T2-SPACE images for better
>>>pial surface reconstruction in the presence of dura -- I was just
>>>wondering if any of that is ready for trial?
>>> 
>>> Thanks!
>>> 
>>> Warren
>>> 
>>> --
>>> Warren Winter
>>> Research Coordinator
>>> Boston Children's Hospital
>>> Sheridan Laboratory of Cognitive Neuroscience
>>> Division of Developmental Medicine
>>> 1 Autumn Street, AU 650
>>> Boston, MA 02215
>>> 857-218-5224
>>> 
>>> 
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>>> 
>>> 
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>> 
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Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

[Matt Glasser]

If you make a T1 map you can use that to look at differences in myelin
content, but I don't know all of the ways to calculate T1 or if you could
get that from only two flip angles.  Two images with roughly the same
contrast won't work for the ratio method.  You need to have opposite
contrast.

Also I'm not sure how a FLAIR would be better than a T2-SPACE.

Peace,

Matt.

From:  Satrajit Ghosh 
Date:  Tuesday, November 20, 2012 5:51 PM
To:  Matt Glasser 
Cc:  "Watson, Christopher" ,
"Winter, Warren" ,
"freesurfer@nmr.mgh.harvard.edu" 
Subject:  Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial
surface recons?

hi 

matt: could you generate the myelin maps say from two flash scans at
different flip angles?

bruce: if one had a choice between an mprage + t2 flair and 2 flash scans at
5/20 flip angles, what would be your recommendation?

cheers,

satra

On Tue, Nov 20, 2012 at 6:35 PM, Matt Glasser  wrote:
> If you get an MPRAGE and T2-SPACE you can make myelin maps too.
> FreeSurfer's final surface placement benefits a lot from high resolution
> images (less than 1mm) and you can still get good SNR with when you use
> 32-channel coils.
> 
> Peace,
> 
> Matt.
> 
> On 11/20/12 4:41 PM, "Bruce Fischl"  wrote:
> 
>> >Yes, definitely. The t2-space flair is a big help
>> >
>> >
>> >
>> >On Nov 20, 2012, at 5:40 PM, "Watson, Christopher"
>> > wrote:
>> >
>>> >> Hi Bruce,
>>> >> So would you recommend acquiring a T2 in addition to an
>>> >>(ME)MPRAGE/SPGR? i.e. is it worth squeezing another acquisition into a
>>> >>protocol?
>>> >>
>>> >> Chris
>>> >> 
>>> >> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> >>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>>> >>[fis...@nmr.mgh.harvard.edu]
>>> >> Sent: Tuesday, November 20, 2012 3:01 PM
>>> >> To: Winter, Warren
>>> >> Cc: freesurfer@nmr.mgh.harvard.edu
>>> >> Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial
>>> >>surface recons?
>>> >>
>>> >> Hi Warren
>>> >>
>>> >> yes, it will be part of the upcoming 5.2 release, hopefully in Dec. It
>>> >> will use either a FLAIR or T2 (ideally T2-SPACE for either one)
>>> >>
>>> >> cheers
>>> >> Bruce
>>> >> On Tue, 20
>>> >> Nov 2012, Winter, Warren wrote:
>>> >>
>>>> >>> Hi all,
>>>> >>>
>>>> >>> Back in January and October Bruce mentioned that he had under
>>>> >>>development some scripts designed to utilize T2-SPACE images for better
>>>> >>>pial surface reconstruction in the presence of dura -- I was just
>>>> >>>wondering if any of that is ready for trial?
>>>> >>>
>>>> >>> Thanks!
>>>> >>>
>>>> >>> Warren
>>>> >>>
>>>> >>> --
>>>> >>> Warren Winter
>>>> >>> Research Coordinator
>>>> >>> Boston Children's Hospital
>>>> >>> Sheridan Laboratory of Cognitive Neuroscience
>>>> >>> Division of Developmental Medicine
>>>> >>> 1 Autumn Street, AU 650
>>>> >>> Boston, MA 02215
>>>> >>> 857-218-5224
>>>> >>>
>>>> >>>
>>>> >>> ___
>>>> >>> Freesurfer mailing list
>>>> >>> Freesurfer@nmr.mgh.harvard.edu
>>>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> >>>
>>>> >>>
>>>> >>>
>>> >> ___
>>> >> Freesurfer mailing list
>>> >> Freesurfer@nmr.mgh.harvard.edu
>>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >>
>>> >>
>>> >> 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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>> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
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Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

[Matt Glasser]

Hi Bruce,

Can you get good FLAIRs at 0.7mm isotropic?

The fluid thing makes sense for surface reconstruction, but I think it
would mess up myelin maps if someone also wanted to do that using the
ratio method.  If the CSF is now dark and you divide the dark CSF in the
T1w with dark CSF in the T2w, you would get unpredictable results in the
partial volume region along the edge.

Thanks,

Matt.

On 11/20/12 6:27 PM, "Bruce Fischl"  wrote:

>Hi Satra
>
>the T1 maps accomplish much of what the ratio does - it gets rid of
>receive bias effects. I'm not really sure which is better. They are about
>the same amount of scan time.
>
>The advantage of including the flair inversion pulse in the T2 space is
>that it nulls fluid and lets intensities by monotonically decreasing
>moving 
>outwards from the gray/white boundary. This makes partial volume effects
>less of a problem. Dura is also pretty much totally absent from the FLAIR
>and in the prelim data that we've processed having the FLAIR images lets
>the surface recover from pretty much all mistakes in which dura is
>included 
>in the pial surface.
>
>cheers
>Bruce
>
>
>
>On Tue, 20 Nov 2012, Matt Glasser wrote:
>
>> If you make a T1 map you can use that to look at differences in myelin
>> content, but I don't know all of the ways to calculate T1 or if you
>>could
>> get that from only two flip angles.  Two images with roughly the same
>> contrast won't work for the ratio method.  You need to have opposite
>> contrast.
>> 
>> Also I'm not sure how a FLAIR would be better than a T2-SPACE.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: Satrajit Ghosh 
>> Date: Tuesday, November 20, 2012 5:51 PM
>> To: Matt Glasser 
>> Cc: "Watson, Christopher" ,
>> "Winter, Warren" ,
>> "freesurfer@nmr.mgh.harvard.edu" 
>> Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial
>> surface recons?
>> 
>> hi 
>> matt: could you generate the myelin maps say from two flash scans at
>> different flip angles?
>> bruce: if one had a choice between an mprage + t2 flair and 2 flash
>>scans at
>> 5/20 flip angles, what would be your recommendation?
>> 
>> cheers,
>> 
>> satra
>> 
>> On Tue, Nov 20, 2012 at 6:35 PM, Matt Glasser  wrote:
>>   If you get an MPRAGE and T2-SPACE you can make myelin maps too.
>>   FreeSurfer's final surface placement benefits a lot from high
>>   resolution
>>   images (less than 1mm) and you can still get good SNR with when
>>   you use
>>   32-channel coils.
>>
>>   Peace,
>>
>>   Matt.
>>
>>   On 11/20/12 4:41 PM, "Bruce Fischl" 
>>   wrote:
>>
>>   >Yes, definitely. The t2-space flair is a big help
>>   >
>>   >
>>   >
>>   >On Nov 20, 2012, at 5:40 PM, "Watson, Christopher"
>>   > wrote:
>>   >
>>   >> Hi Bruce,
>>   >> So would you recommend acquiring a T2 in addition to an
>>   >>(ME)MPRAGE/SPGR? i.e. is it worth squeezing another
>>   acquisition into a
>>   >>protocol?
>>   >>
>>   >> Chris
>>   >> 
>>   >> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>   >>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce
>>   Fischl
>>   >>[fis...@nmr.mgh.harvard.edu]
>>   >> Sent: Tuesday, November 20, 2012 3:01 PM
>>   >> To: Winter, Warren
>>   >> Cc: freesurfer@nmr.mgh.harvard.edu
>>   >> Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE
>>   data in pial
>>   >>surface recons?
>>   >>
>>   >> Hi Warren
>>   >>
>>   >> yes, it will be part of the upcoming 5.2 release, hopefully
>>   in Dec. It
>>   >> will use either a FLAIR or T2 (ideally T2-SPACE for either
>>   one)
>>   >>
>>   >> cheers
>>   >> Bruce
>>   >> On Tue, 20
>>   >> Nov 2012, Winter, Warren wrote:
>>   >>
>>   >>> Hi all,
>>   >>>
>>   >>> Back in January and October Bruce mentioned that he had
>>   under
>>   >>>development some scripts designed to utilize T2-SPACE images
>>   for better
>>   &

Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

[Matt Glasser]

You can correct the readout distortion with a field map.  The main
residual is just signal loss in the gradient echo image.

Peace,

Matt.

On 11/20/12 7:22 PM, "Bruce Fischl"  wrote:

>sure. Note that whichever you do it's absolutely critical to bandwidth
>and readout match them so there is no differential distortion between the
>contrast types
>Bruce
>On Tue, 20 Nov 2012, Satrajit Ghosh wrote:
>
>> thanks matt and bruce. this is very helpful.
>> cheers,
>> 
>> satra
>> 
>> On Tue, Nov 20, 2012 at 7:53 PM, Bruce Fischl
>>
>> wrote:
>>   yes, that's probably true. The FLAIR we use is just a T2-SPACE
>>   scan with an inversion pulse to put CSF at the null point, so if
>>   you can get T2-space at .7 you should be able to get FLAIR
>>   (although you do burn some SNR with the inversion)
>>
>>   On Tue, 20 Nov 2012, Matt Glasser wrote:
>>
>> Hi Bruce,
>>
>> Can you get good FLAIRs at 0.7mm isotropic?
>>
>> The fluid thing makes sense for surface
>> reconstruction, but I think it
>> would mess up myelin maps if someone also wanted to
>> do that using the
>> ratio method.  If the CSF is now dark and you divide
>> the dark CSF in the
>> T1w with dark CSF in the T2w, you would get
>> unpredictable results in the
>> partial volume region along the edge.
>>
>> Thanks,
>>
>> Matt.
>>
>> On 11/20/12 6:27 PM, "Bruce Fischl"
>>  wrote:
>>
>>   Hi Satra
>>
>>   the T1 maps accomplish much of what the
>>   ratio does - it gets rid of
>>   receive bias effects. I'm not really
>>   sure which is better. They are about
>>   the same amount of scan time.
>>
>>   The advantage of including the flair
>>   inversion pulse in the T2 space is
>>   that it nulls fluid and lets intensities
>>   by monotonically decreasing
>>   moving
>>   outwards from the gray/white boundary.
>>   This makes partial volume effects
>>   less of a problem. Dura is also pretty
>>   much totally absent from the FLAIR
>>   and in the prelim data that we've
>>   processed having the FLAIR images lets
>>   the surface recover from pretty much all
>>   mistakes in which dura is
>>   included
>>   in the pial surface.
>>
>>   cheers
>>   Bruce
>> 
>> 
>>
>>   On Tue, 20 Nov 2012, Matt Glasser wrote:
>>
>> If you make a T1 map you can
>> use that to look at
>> differences in myelin
>> content, but I don't know
>> all of the ways to calculate
>> T1 or if you
>> could
>> get that from only two flip
>> angles.  Two images with
>> roughly the same
>> contrast won't work for the
>>     ratio method.  You need to
>> have opposite
>> contrast.
>>
>> Also I'm not sure how a
>> FLAIR would be better than a
>> T2-SPACE.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Satrajit Ghosh
>> 
>> Date: Tuesday, November 20,
>> 2012 5:51 PM
>> To: Matt Glasser
>> 
>> Cc: "Watson, Christopher"
>> ,
>> "Winter, Warren"
>> ,
>> "freesurfer@nmr.mgh.harvard.edu"
>> 
>> Subject: Re: [Freesurfer]
>> Tool for incorporating
>>

Re: [Freesurfer] How can I get 300 dpi resolution or about when saving tiff files in tksurfer?

[Matt Glasser]

Perhaps you can maximize the tksurfer window on a large monitor, take a
whole screen screenshot, and then in a photo editing program: decrease the
physical size of the image (in mm or inches) while not decreasing the
matrix size.  You can do this in photoshop in Image > Image Size > And
then change the document size until the resolution is 300.  This will
increase the DPI to make nice figures.  What Bruce suggests will just
upsample the image (without adding detail), which is not what journals
have in mind when they ask for 300dpi figures.  Keep in mind that the
document size is the printable size, so your image will get smaller on the
printed page when you do this.  Often, figures have multiple panels and if
you take each panel as a full screen image on a large monitor and then
reduce the size you will have more than 300dpi to spare in the end result.
 

Peace,

Matt.

On 12/6/12 3:22 PM, "Bruce Fischl"  wrote:

>Hi Knut
>the tiffs written by tksurfer are 600x600 regardless of what DPI you set.
>You can change the dpi with convert (or photoshop), but it won't change
>the 
># of pixels.
>
>cheers
>Bruce
>
>
>On Thu, 6 Dec 2012, Knut J Bjuland wrote:
>
>>
>>   How can I get 300 dpi resolution or about when saving tiff files in
>> tksurfer?
>> ___
>> 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
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
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Re: [Freesurfer] unusually long running time in autorecon2

[Matt Glasser]

I've noticed this at well when something goes wrong before mri_cc.  It gets
stuck in some kind of infinite loop.  You might check that the linear and
nonlinear registration worked correctly.

Peace,

Matt.

From:  Dawei Liu 
Date:  Wednesday, February 20, 2013 10:49 AM
To:  
Subject:  [Freesurfer] unusually long running time in autorecon2


Dear Freesurfer experts,
 
I am running autorecon2 using Freesurfer verion 5.1.0 on Linux. For some
subjects, it looks that the pipeline stucked in the middle of  mri_cc and
keeps running for days (without any error message). Last time when it
occurred I thought it may be caused by some hardware-related problem, so I
killed these jobs and re-launched recon-all -autorecon2 on a different
machine. Now these jobs have been running for over 40 hours and they are
still running. Do you know why they take so long? For your reference,  I
copied the most recent processing information below:
 
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta
/Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_344
79/mri/transforms/cc_up.lta 0057_34479
 
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as 
/Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_344
79/mri/transforms/cc_up.lta
reading aseg from 
/Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_344
79/mri/aseg.auto_noCCseg.mgz
reading norm from 
/Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_344
79/mri/norm.mgz
24076 voxels in left wm, 23641 in right wm, xrange [73, 130]
searching rotation angles z=[65 79], y=[-54 -40]
searching scale 1 Z rot 75.6  global minimum found at slice 103.0, rotations
(-50.09, 68.60)
final transformation (x=103.0, yr=-50.093, zr=68.597):
0.234  -0.931  -0.280   230.831;
0.597   0.365  -0.714   75.219;
0.767  -0.000   0.642   3.440;
0.000   0.000   0.000   1.000;
 
Thanks in advance for your help!
 
Dawei
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Re: [Freesurfer] High resolution fMRI and resolution of anatomical scans

[Matt Glasser]

I'd collect highres T1w as well and then refine the 1mm surfaces using that.

Peace,

Matt.

From:  SHAHIN NASR 
Date:  Monday, February 25, 2013 1:39 PM
To:  Freesurfer , Bruce Fischl
, Doug Greve 
Subject:  [Freesurfer] High resolution fMRI and resolution of anatomical
scans

Hi,
We are planning to collect high resolution functional MRI for a group of
subjects with voxel size smaller than 1 mm. For these subjects, we already
have reconstructed anatomical scans with 1 mm voxel size. The question is,
do we need to re-collect anatomical scans for these subjects with smaller
voxel size (e.g. 0.5 x 0.5 x 0.5) or we can still use the old anatomical
data for co-registration with freesurfer.

P.S.: We usually analyze our subjects in native space but technically we can
do this in fsaverage space.  So, we only need this co-registration for
pre-processing and mapping fMRI data to fsaverage space.

Regards


-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] Advice on integrating FSL's BET with recon-all

[Matt Glasser]

I would check the mri_em_register registrations of the step that
immediately precedes mri_watershed (and produces
talairach_with_skull.lta).  We found that most of the variability and
failures occurred in this step, and mri_watershed itself is a very robust
brain extraction algorithm when it is given an accurate registration (my
experience with BET is that it is probably not the best tool for getting
very accurate brainmasks and sometimes takes away too much). I would
recommend using the BET extracted image instead of the image with skull
for the initial registration step, and then you can use mri_watershed on
the original image and get good results every time.  This is the type of
strategy we use in the HCP Pipelines (except we use something more robust
than BET for the initial mask).

Note that the "talairach" registration (done by the -talairach step with
the talairach_avi tool) has nothing to do with the registration that
precedes brain extraction.  Perhaps it should is more robust and should be
used, but the affine would have to be converted to the correct format.

Peace,

Matt.

On 3/6/13 3:53 PM, "Bruce Fischl"  wrote:

>you can use
>
>mri_convert -rl ...
>
>to reslice the output of bet so that it has the same geometry as the rest
>of our stream
>
>cheers
>Bruce
>
>On Wed, 6 Mar 2013, Winter, Warren wrote:
>
>> Hi again,
>> We have had some suboptimal results from FreeSurfer's skullstripping
>>algorithm, even after iteratively trying different
>> watershed thresholds and after checking the quality of Talairach
>>registration.  The results are pretty good, but often leave
>> some dura matter and bits of neck behind whose higher intensity values,
>>I believe, may end up skewing recon-all's later
>> estimation of the range of intensity values within grey matter, and
>>consequently compromising the accuracy of pial surface
>> estimation.
>> 
>> FSL's BET, however, seems to do a better job of extracting the brain,
>>at least for our dataset.  So, I was wondering if I
>> might be able to skip over mri_watershed and feed autorecon2 and
>>autorecon3 a brainmask.mgz file created using BET.  I tried
>> this procedure:
>> 
>> 
>> 1) mri_convert  T1.nii.gz
>> 2) bet T1.nii.gz BET_brainmask.nii.gz -A
>> 3) mri_convert BET_brainmask.nii.gz BET_brainmask.mgz
>> 4) recon-all -s  -autorecon1 -noskullstrip
>> 5) mv BET_brainmask.nii.gz .//mri/brainmask.mgz
>> 6) recon-all -s  -autorecon2 -autorecon3
>> 
>> And I got this error message, right after normalization2:
>> 
>> "
>> #@# Mask BFS Tue Mar  5 22:52:05 EST 2013
>> 
>>/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/20
>>12_bet/mri
>> 
>>  mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
>> 
>> threshold mask volume at 5
>> ERROR: dimension mismatch between source and mask
>> Linux rc-thunderball 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012
>>x86_64 x86_64 x86_64 GNU/Linux
>> 
>> recon-all -s 2012_bet exited with ERRORS at Tue Mar  5 22:52:06 EST 2013
>> "
>> 
>> I'm guessing that the dimensions of norm.mgz and aseg.mgz didn't match
>>those of brainmask.mgz, resulting during normalization2
>> in a mismatch between brain.mgz and brainmask.mgz.  Does that seem
>>right, and is there a possible workaround?
>> 
>> Thank you!
>> 
>> Warren
>> 
>> --
>> Warren Winter
>> Research Coordinator
>> Boston Children's Hospital
>> Sheridan Laboratory of Cognitive Neuroscience
>> Division of Developmental Medicine
>> 1 Autumn Street, AU 650
>> Boston, MA 02215
>> 857-218-5224
>> 
>> 
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Re: [Freesurfer] Caret to Freesurfer

[Matt Glasser]

She wants to go from Caret to FreeSurfer, rather than from FreeSurfer to
Caret, which is what I do.

Kara, I believe we are meeting tomorrow to discuss the options for this?

I don't know anything about the FreeSurfer longitudinal pipeline, but it
would take going through the pipeline and finding all of the inputs needed
and converting them or generating them.  I think the main goal here is to
use the longitudinal surface registration.

Matt.

On 3/14/13 8:04 PM, "Bruce Fischl"  wrote:

>Hi Kara
>
>I think the answer is yes as there are people at Wash U that do this
>routinely. Maybe Matt Glasser or someone else can chime in?
>
>cheers
>Bruce
>
>
>On Thu, 14 Mar 2013, Ellspermann, Kara wrote:
>
>> I am new to Freesurfer, and I am trying to input/process preterm infant
>> brain data (ultimately attempting longitudinal registration). I already
>>have
>> surfaces generated from Caret, as well as the original T1/T2 images.  My
>> question is: Does anything exist to take processed data from Caret into
>> Freesurfer?  If not, is there a good way to process the T1/T2 images in
>> Freesurfer despite the differences in contrast and intensity (and
>>anatomy)? 
>> 
>> Thank you in advance for your advice,
>> Kara
>> 
>>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>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] Very different results between 5.1.0 and 5.2.0

[Matt Glasser]

Do the surfaces look correct in these regions?  You might post some
screenshots of subjects who have a big difference between 5.1 and 5.2 with
the 5.1 and 5.2 white and pial surfaces on volume slices that highlight
the difference.  Without this kind of info, its hard to know which was
more correct, 5.1 or 5.2.

Peace,

Matt.

On 3/18/13 5:13 PM, "Ritobrato Datta"  wrote:

>I concur. I have seen similar results in primary visual cortex from ~40
>subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to
>1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3.
>
>Ritobrato Datta, Ph.D.
>Post Doctoral Researcher
>Department of Neurology
>University of Pennsylvania School of Medicine
>3rd Floor, Room 312
>3710 Hamilton Walk (Goddard Laboratories)
>Philadelphia, PA 19104-6241
>email - rida...@mail.med.upenn.edu
> 
>
>- Original Message -
>From: Daniel Yang 
>To: freesurfer@nmr.mgh.harvard.edu
>Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT)
>Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0
>
>Dear FreeSurfer Experts,
>
>I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161
>subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in
>particular.
>
>Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in
>5.2.0. They are significantly different, t(160) = 56.71.
>
>The correlation between the two versions is r = .33
>
>Is this something possible?? I can't see what went wrong in my procedures.
>
>Thanks!
>Daniel
>
>--
>Yung-Jui "Daniel" Yang, PhD
>Postdoctoral Researcher
>Yale Child Study Center
>New Haven, CT
>(203) 737-5454
>
>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>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] license file not working

[Matt Glasser]

They updated the format so you have to get another.

Peace,

Matt.

On 2/2/17, 2:13 PM, "Anthony Dick"  wrote:

>Hello,
>
>I have been using Freesurfer for a number of years, and just installed
>v6.0. I run into this problem:
>
>--
>ERROR: Invalid FreeSurfer license key found in license file
>/Applications/freesurfer/.license
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
>--
>
>I have a valid .license file, in the Freesurfer home directory
>
>Last login: Thu Feb  2 15:04:01 on ttys005
> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>Setting up environment for FreeSurfer/FS-FAST (and FSL)
>FREESURFER_HOME   /Applications/freesurfer
>FSFAST_HOME   /Applications/freesurfer/fsfast
>FSF_OUTPUT_FORMAT nii.gz
>SUBJECTS_DIR  /Applications/freesurfer/subjects
>MNI_DIR   /Applications/freesurfer/mni
>[38c9862eb0b0:~] adick% cd /Applications/freesurfer
>[38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>-rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>[38c9862eb0b0:/Applications/freesurfer] adick%
>
>Any ideas?
>
>Thanks!
>
>Anthony
>
>
>-- 
>Anthony Steven Dick, Ph.D.
>Associate Professor
>Director, Cognitive Neuroscience Program and Graduate Certificate in
>Cognitive Neuroscience
>Department of Psychology
>Florida International University Modesto A. Maidique Campus AHC4 454
>11200 S.W. 8th Street
>Miami, FL 33199
>Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
>Email: ad...@fiu.edu
>Webpage: http://myweb.fiu.edu/adick
>Join the Society for the Study of Human Development:
>http://www.sshdonline.org
>
>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>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] license file not working

[Matt Glasser]

Like I said, they changed the format at some point and stopped accepting the
old format with FS 6.0.  I have used FreeSurfer for a long time too and
found that I had to get a new license file with this version.

Peace,

Matt.

From:   on behalf of Anthony Dick

Reply-To:  Freesurfer support list 
Date:  Thursday, February 2, 2017 at 5:18 PM
To:  
Subject:  Re: [Freesurfer] license file not working


 

Hello,
 

I have used my old file, registered under two different emails (and received
the code and made new files each time, named both .license and license.txt).
Restarted the computer etc. I am wondering if it is a permissions issue. It
seems to be finding the file where I put it. Have never encountered this
issue and have been using Freesurfer for 11 years. If history is any guide,
it will probably turn out to be something stupid that I did :)
 

Anthony
 
 
 
On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
 
 
>   
> The .license that it comes with is not the same as the license.txt that you
> have to acquire. I was able to use an old license.txt from my Freesurfer 5.3
> for 6.0. 
> 
>  
>  
> Best
>  
> 
>  
>  
> Trisanna
>  
>  
> 
>  
>  
>  
>  
>  
> --
>  
> Ph.D. Candidate 
> McGill University
>   
> Integrated Program in Neuroscience
>  
> Psychology
>  
> 
>  
>  
>  
>  
>  
>  
>  
>  
>  
> On Thu, Feb 2, 2017 at 3:21 PM, X K  wrote:
>  
>>  
>> try to rename the file to license.txt?
>>  
>>  
>>  
>> 
>>  
>> On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick  wrote:
>>  
>>> Hello,
>>>  
>>>  I have been using Freesurfer for a number of years, and just installed
>>>  v6.0. I run into this problem:
>>>  
>>>  --
>>>  ERROR: Invalid FreeSurfer license key found in license file
>>>  /Applications/freesurfer/.license
>>> If you are outside the NMR-Martinos Center,
>>> go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>>> get a valid license file (it's free).
>>> If you are inside the NMR-Martinos Center,
>>> make sure to source the standard environment.
>>>  --
>>>  
>>>  I have a valid .license file, in the Freesurfer home directory
>>>  
>>>  Last login: Thu Feb  2 15:04:01 on ttys005
>>>   freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>>>  Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>>  FREESURFER_HOME   /Applications/freesurfer
>>>  FSFAST_HOME   /Applications/freesurfer/fsfast
>>>  FSF_OUTPUT_FORMAT nii.gz
>>>  SUBJECTS_DIR  /Applications/freesurfer/subjects
>>>  MNI_DIR   /Applications/freesurfer/mni
>>>  [38c9862eb0b0:~] adick% cd /Applications/freesurfer
>>>  [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>>>  -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>>>  [38c9862eb0b0:/Applications/freesurfer] adick%
>>>  
>>>  Any ideas?
>>>  
>>>  Thanks!
>>>  
>>>  Anthony
>>>  
>>>  
>>>  --
>>>  Anthony Steven Dick, Ph.D.
>>>  Associate Professor
>>>  Director, Cognitive Neuroscience Program and Graduate Certificate in
>>> Cognitive Neuroscience
>>>  Department of Psychology
>>>  Florida International University Modesto A. Maidique Campus AHC4 454
>>>  11200 S.W. 8th Street
>>>  Miami, FL 33199
>>>  Ph: 305-348-4202  ; Lab Ph: 305-348-9055
>>>  ; Fx: 305-348-3879 
>>>  Email: ad...@fiu.edu
>>>  Webpage: http://myweb.fiu.edu/adick
>>>  Join the Society for the Study of Human Development:
>>> http://www.sshdonline.org
>>>  
>>>  ___
>>>  Freesurfer mailing list
>>>  Freesurfer@nmr.mgh.harvard.edu
>>>  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>  
>>>  
>>>  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.
>>>  
>>>  
>>  
>>  
>>  
>>  
>> 
>>  
>>  
>>  
>>  -- 
>>  
>>  
>> -
>> 
>>  
>> Kong Xiangzhen
>>  State Key Laboratory of Cognitive Neuroscience and Learning,
>>  Beijing Normal University,
>>  Beijing, China, 100875.
>>  
>>  
>>  ___
>>  Freesurfer mailing list
>>  Freesurfer@nmr.mgh.harvard.edu
>>  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>  
>>  
>>  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.o

Re: [Freesurfer] license file not working

[Matt Glasser]

Strange, that fixed things right up for me.  You might make sure you know
where you are calling FreeSurfer from and that there are no old license
files lying around.

Peace,

Matt.

From:   on behalf of Anthony Dick

Reply-To:  Freesurfer support list 
Date:  Thursday, February 2, 2017 at 5:46 PM
To:  
Subject:  Re: [Freesurfer] license file not working


 

Thanks Matt. I already tried it with a new registration, but it doesn't hurt
to try it again. That may be where the issue is. I'll post if that turns out
to be the problem. Thanks!
 

Anthony
 
 
 
On 2/2/17 6:28 PM, Matt Glasser wrote:
 
 
>   
> Like I said, they changed the format at some point and stopped accepting the
> old format with FS 6.0.  I have used FreeSurfer for a long time too and found
> that I had to get a new license file with this version.
>  
> 
>  
>  
> Peace,
>  
> 
>  
>  
> Matt.
>  
> 
>  
>   
> From:   on behalf of Anthony Dick
> 
>  Reply-To:  Freesurfer support list 
>  Date:  Thursday, February 2, 2017 at 5:18 PM
>  To:  
>  Subject:  Re: [Freesurfer] license file not working
>  
>  
> 
>  
>  
>  
>  
> 
> Hello,
>  
> 
> I have used my old file, registered under two different emails (and received
> the code and made new files each time, named both .license and license.txt).
> Restarted the computer etc. I am wondering if it is a permissions issue. It
> seems to be finding the file where I put it. Have never encountered this issue
> and have been using Freesurfer for 11 years. If history is any guide, it will
> probably turn out to be something stupid that I did :)
>  
> 
> Anthony
>  
>  
>  
> On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
>  
>  
>>  
>> The .license that it comes with is not the same as the license.txt that you
>> have to acquire. I was able to use an old license.txt from my Freesurfer 5.3
>> for 6.0. 
>> 
>>  
>>  
>> Best
>>  
>> 
>>  
>>  
>> Trisanna
>>  
>>  
>> 
>>  
>>  
>>  
>>  
>>  
>> --
>>  
>> Ph.D. Candidate 
>> McGill University
>>   
>> Integrated Program in Neuroscience
>>  
>> Psychology
>>  
>> 
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>> On Thu, Feb 2, 2017 at 3:21 PM, X K  wrote:
>>  
>>>  
>>> try to rename the file to license.txt?
>>>  
>>>  
>>>  
>>> 
>>>  
>>> On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick  wrote:
>>>  
>>>> Hello,
>>>>  
>>>>  I have been using Freesurfer for a number of years, and just installed
>>>>  v6.0. I run into this problem:
>>>>  
>>>>  --
>>>>  ERROR: Invalid FreeSurfer license key found in license file
>>>>  /Applications/freesurfer/.license
>>>> If you are outside the NMR-Martinos Center,
>>>> go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>>>> get a valid license file (it's free).
>>>> If you are inside the NMR-Martinos Center,
>>>> make sure to source the standard environment.
>>>>  --
>>>>  
>>>>  I have a valid .license file, in the Freesurfer home directory
>>>>  
>>>>  Last login: Thu Feb  2 15:04:01 on ttys005
>>>>   freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>>>>  Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>>>  FREESURFER_HOME   /Applications/freesurfer
>>>>  FSFAST_HOME   /Applications/freesurfer/fsfast
>>>>  FSF_OUTPUT_FORMAT nii.gz
>>>>  SUBJECTS_DIR  /Applications/freesurfer/subjects
>>>>  MNI_DIR   /Applications/freesurfer/mni
>>>>  [38c9862eb0b0:~] adick% cd /Applications/freesurfer
>>>>  [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>>>>  -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>>>>  [38c9862eb0b0:/Applications/freesurfer] adick%
>>>>  
>>>>  Any ideas?
>>>>  
>>>>  Thanks!
>>>>  
>>>>  Anthony
>>>>  
>>>>  
>>>>  --
>>>>  Anthony Steven Dick, Ph.D.
>>>>  Associate Professor
>>>>  Director, Cognitive Neuroscience Program and Graduate Certificate in
>>>> Cognitive Neuroscience
>>&

Re: [Freesurfer] license file not working

[Matt Glasser]

No worries Bruce!

Matt.

On 2/3/17, 12:52 PM, "Bruce Fischl"
 wrote:

>Hi Matt
>
>just to clarify - our old license format stopped working with newer
>versions of libcrypt and so we were forced to change to the new format.
>It 
>was not done gratuitously on our part or as a way to get people to
>request 
>new licenses - we had no choice.
>
>cheers
>Bruce
>
>
>On Thu, 2 Feb 2017, Matt Glasser wrote:
>
>> Like I said, they changed the format at some point and stopped
>>accepting the old format with FS 6.0.  I
>> have used FreeSurfer for a long time too and found that I had to get a
>>new license file with this
>> version.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From:  on behalf of Anthony
>>Dick 
>> Reply-To: Freesurfer support list 
>> Date: Thursday, February 2, 2017 at 5:18 PM
>> To: 
>> Subject: Re: [Freesurfer] license file not working
>> 
>> Hello,
>> 
>> I have used my old file, registered under two different emails (and
>>received the code and made new files
>> each time, named both .license and license.txt). Restarted the computer
>>etc. I am wondering if it is a
>> permissions issue. It seems to be finding the file where I put it. Have
>>never encountered this issue and
>> have been using Freesurfer for 11 years. If history is any guide, it
>>will probably turn out to be
>> something stupid that I did :)
>> 
>> Anthony
>> 
>> 
>> On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
>>   The .license that it comes with is not the same as the
>>license.txt that you have to acquire.
>>   I was able to use an old license.txt from my Freesurfer 5.3 for
>>6.0.
>> Best
>> 
>> Trisanna
>> 
>> --
>> Ph.D. Candidate McGill University
>> Integrated Program in Neuroscience
>> Psychology
>> 
>> 
>> On Thu, Feb 2, 2017 at 3:21 PM, X K  wrote:
>>   try to rename the file to license.txt?
>> 
>> On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick  wrote:
>>   Hello,
>>
>>   I have been using Freesurfer for a number of years, and just
>>installed
>>   v6.0. I run into this problem:
>>
>>   
>>-
>>-
>>   ERROR: Invalid FreeSurfer license key found in license file
>>   /Applications/freesurfer/.license
>>  If you are outside the NMR-Martinos Center,
>>  go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>>  get a valid license file (it's free).
>>  If you are inside the NMR-Martinos Center,
>>  make sure to source the standard environment.
>>   
>>-
>>-
>>
>>   I have a valid .license file, in the Freesurfer home directory
>>
>>   Last login: Thu Feb  2 15:04:01 on ttys005
>>    freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>>   Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>   FREESURFER_HOME   /Applications/freesurfer
>>   FSFAST_HOME   /Applications/freesurfer/fsfast
>>   FSF_OUTPUT_FORMAT nii.gz
>>   SUBJECTS_DIR  /Applications/freesurfer/subjects
>>   MNI_DIR   /Applications/freesurfer/mni
>>   [38c9862eb0b0:~] adick% cd /Applications/freesurfer
>>   [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>>   -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>>   [38c9862eb0b0:/Applications/freesurfer] adick%
>>
>>   Any ideas?
>>
>>   Thanks!
>>
>>   Anthony
>> 
>>
>>   --
>>   Anthony Steven Dick, Ph.D.
>>   Associate Professor
>>   Director, Cognitive Neuroscience Program and Graduate Certificate
>>in Cognitive
>>   Neuroscience
>>   Department of Psychology
>>   Florida International University Modesto A. Maidique Campus AHC4
>>454
>>   11200 S.W. 8th Street
>>   Miami, FL 33199
>>   Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
>>   Email: ad...@fiu.edu
>>   Webpage: http://myweb.fiu.edu/adick
>>   Join the Society for the Study of Human Development:
>>http://www.sshdonline.org
>>
>>   ___
>>   Freesurfer mailing list
>>   Freesurfer@nmr.mgh.harvard.edu
>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>&

Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

[Matt Glasser]

Since I believe you said you are using my code, I would recommend to stick
with 5.3 at this time.

Peace,

Matt.

From:   on behalf of Antonin Skoch

Reply-To:  Freesurfer support list 
Date:  Tuesday, February 7, 2017 at 2:59 PM
To:  
Subject:  Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much
more externally in comparison to v5.3

Dear Bruce,

thank you for the feedback. I would definitely be interested in 6.1 beta.
What is the approximate timeline of release?
We are working on quite large project (involving -FLAIRpial) and I have to
decide whether to go to v6.0 or to stick with v5.3.
Do you think that so far the 5.3 version is better for T2/FLAIR? Why this is
the case?

Antonin

Hi Antonin

yes, 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. We can give you a beta soon if you like.
cheers
Bruce
  On Tue, 7 
Feb 2017, Antonin Skoch wrote:

> Dear experts,
> 
> I have reprocessed my groups of subjects (originally processed by v5.3) by
> v6.0. I am using -FLAIRpial for pial surface refinement.
> 
> I have noticed that the pial surfaces in v6.0 after -FLAIRpial are positioned
> much more externally in comparison to -FLAIRpial in v5.3. The v6.0 version
> includes to pial sheet much more partial volume voxels in
> comparison to v5.3.
> 
> In contrast to v5.3, where the surfaces after -FLAIRpial were mostly
> internally with respect to pial surfaces determined by T1, in v6.0 there are
> many regions where the pial surfaces after -FLAIRpial are placed
> much externally with respect to pial surfaces determined by T1.
> 
> See the screenshot (red surfaces are pial surfaces after -FLAIRpial with
> v6.0, yellow are surfaces after -FLAIRpial with v.5.3).
> 
> I have used -nsigma_above 8 in mris_make_surfaces to prevent excluding some
> cortical regions with high signal intensity but this I used consistently in
> both versions so it should not be the reason of difference.
> 
> I have uploaded the subject processed both by 5.3 and 6.0 version to your
> server, files FLAIRpial_v5.3.tar.gz and FLAIRpial_v6.0.tar.gz.
> 
> Could you please look at my data and check whether the pial surfaces after
> -FLAIRpial in v6.0 look OK from your perspective?
> 
> Regards,
> 
> Antonin Skoch
___ Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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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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.

Re: [Freesurfer] issues with -T2pial option in v.5.3

[Matt Glasser]

You could try with the HCP Pipelines and see if that helps:

https://github.com/Washington-University/Pipelines

Peace,

Matt.

From:   on behalf of Petr Bednarik

Reply-To:  Freesurfer support list 
Date:  Monday, February 20, 2017 at 12:26 PM
To:  
Subject:  [Freesurfer] issues with -T2pial option in v.5.3

Hi everyone, 

I am using Freesurfer version 5.3. I tried to refine the pial surfaces by
using  -T2pial option:

recon-all -subjid $SUBJ -T2/SUBJECT_DIR/$SUBJ/mri/orig/T2raw.mgz -T2pial
-autorecon3 

This step was helpful - e.g. it removed nicely residuals of venous sinuses,
but in some subjects it also removed part of the parietal or frontal cortex,
while the white matter is appropriately segmented.

https://www.dropbox.com/s/4gzsvrg85xsfdkn/surfaces_over_brainmask.mgz.png?dl
=0

The T2-space images had the same resolution as T1-MPRAGE (1x1x1mm) and were
acquired in the same session (3T Siemens Trio, standard 32 channel coil).
The problem does not seem to be caused by T2 misregistration :

https://www.dropbox.com/s/a7gdpxom0cqgj1u/surfaces_over_T2.mgz.png?dl=0

Question : What could cause this error and how could I extend pial surfaces
and get correct final segmentation ?

Thanks a lot !

PB
   
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Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

[Matt Glasser]

Not yet.  We are hoping FreeSurfer 6.1 will work nicely with the HCP
Pipelines.  For now version 6.0 has some regressions as far as surface
placement goes and there are also some adaptations we need to make to the
pipelines.  

Peace,

Matt.

From:   on behalf of CAGNA Bastien

Reply-To:  Freesurfer support list 
Date:  Monday, March 13, 2017 at 7:21 AM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Can we use fressurfer 6 with the Human connectome
project's pipeline ?

Dear freesurfer experts,



I'm wondering if it's possible to run the human connetome project's minimal
processing pipeline using freesurfer 6 ?



Does it require some update of the pipeline or is there anybody that have
already enjoyed the new freesurfer version with this pipeline ?



Thank you for your attention and your help,

Bastien Cagna




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Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

[Matt Glasser]

Hi Bruce,

I don¹t think the hires T1w and T2w stuff are as accurate as 5.3 in the
HCP 0.7mm data that I have looked at (and as I recall at least one other
user had some similar issues, as did one of my collaborators), but that
was all I meant to refer to.  Sorry if my reply came across more general
than that, as of course we want to move to using FreeSurfer V6+ in the
future.  It is the highres T1w and T2w stuff that my pipelines are
designed to exploit, however.  Also there are some changes I have to make
to the HCP Pipelines for FreeSurfer V6+ because of differing file names,
etc.

Best,

Matt.

On 3/13/17, 9:40 PM, "Bruce Fischl"
 wrote:

>Hi Matt
>
>To state without qualification that "6.0 has some regressions as far as
>surface placement" is incorrect. We quantified its test-retest
>reliability, 
>accuracy and power to detect disease effects and all were improved
>relative 
>to 5.3. We tested V6 on hundreds of datasets across an array of
>pathologies 
>and different MR sequences, field strengths and scanners. We visually
>inspected dozens of brains multiple times in the process of improving
>accuracy and robustness. I can believe that on Wash U HCP data there
>could 
>be some specific issues, but to imply that V6 is generally less accurate
>is 
>simply incorrect.
>
>cheers
>Bruce
>
>
>On Mon, 13 Mar 2017, Matt Glasser wrote:
>
>> Not yet.  We are hoping FreeSurfer 6.1 will work nicely with the HCP
>> Pipelines.  For now version 6.0 has some regressions as far as surface
>> placement goes and there are also some adaptations we need to make to
>>the
>> pipelines.  
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From:  on behalf of CAGNA
>>Bastien
>> 
>> Reply-To: Freesurfer support list 
>> Date: Monday, March 13, 2017 at 7:21 AM
>> To: "freesurfer@nmr.mgh.harvard.edu" 
>> Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome
>> project's pipeline ?
>> 
>> Dear freesurfer experts,
>> 
>> 
>> I'm wondering if it's possible to run the human connetome project's
>>minimal
>> processing pipeline using freesurfer 6 ?
>> 
>> 
>> Does it require some update of the pipeline or is there anybody that
>>have
>> already enjoyed the new freesurfer version with this pipeline ?
>> 
>> 
>> Thank you for your attention and your help,
>> 
>> Bastien Cagna
>> 
>> 
>> 
>> ___ Freesurfer mailing list
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>>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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>>in
>> error but does not contain patient information, please contact the
>>sender
>> and properly dispose of the e-mail.
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>
>The information in this e-mail is intended only for the person to whom it
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>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
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Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

[Matt Glasser]

With FreeSurfer V6.1.

Peace,

Matt.

From:   on behalf of CAGNA Bastien

Reply-To:  Freesurfer support list 
Date:  Tuesday, March 14, 2017 at 11:32 AM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome
project's pipeline ?

Hi everyone,
Thanks for all your answers Bruce, Matt and Antonin.


Matt, may I ask you when do you think that a freesurfer6-compliant version
of the pipeline will be available ?



Best regards,

Bastien 

On 3/13/17, 9:40 PM, "Bruce Fischl"
 wrote:
>Hi Matt
>
>To state without qualification that "6.0 has some regressions as far as
>surface placement" is incorrect. We quantified its test-retest
>reliability, 
>accuracy and power to detect disease effects and all were improved
>relative 
>to 5.3. We tested V6 on hundreds of datasets across an array of
>pathologies 
>and different MR sequences, field strengths and scanners. We visually
>inspected dozens of brains multiple times in the process of improving
>accuracy and robustness. I can believe that on Wash U HCP data there
>could 
>be some specific issues, but to imply that V6 is generally less accurate
>is 
>simply incorrect.
>
>cheers
>Bruce
>
>
>On Mon, 13 Mar 2017, Matt Glasser wrote:
>
>> Not yet. We are hoping FreeSurfer 6.1 will work nicely with the HCP
>> Pipelines. For now version 6.0 has some regressions as far as surface
>> placement goes and there are also some adaptations we need to make to
>>the
>> pipelines. 
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From:  on behalf of CAGNA
>>Bastien
>> 
>> Reply-To: Freesurfer support list 
>> Date: Monday, March 13, 2017 at 7:21 AM
>> To: "freesurfer@nmr.mgh.harvard.edu" 
>> Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome
>> project's pipeline ?
>> 
>> Dear freesurfer experts,
>> 
>> 
>> I'm wondering if it's possible to run the human connetome project's
>>minimal
>> processing pipeline using freesurfer 6 ?
>> 
>> 
>> Does it require some update of the pipeline or is there anybody that
>>have
>> already enjoyed the new freesurfer version with this pipeline ?
>> 
>> 
>> Thank you for your attention and your help,
>> 
>> Bastien Cagna
>> 
>> 
>> 
>> ___ Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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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>
>
>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] difference in T1 and T2 resolution

[Matt Glasser]

What was the error message?

Peace,

Matt.

From:   on behalf of John Anderson

Reply-To:  Freesurfer support list 
Date:  Sunday, June 11, 2017 at 9:06 AM
To:  
Subject:  [Freesurfer] difference in T1 and T2 resolution

Dear Freesurfer experts,
I have T1 and T2 images were unfortunately acquired with different
resolution (i.e the voxel sizes is not the same)
T1 is 280X280X208
T2 is 270X270X200

I tried to run "recon-all"  but it failed to process the data. The command
that I used is :
pbsubmit -c " recon-all -subjid subj1 -T2  PATH_TO_/T2.nii.gz -qcache
-T2pial -all" 
 
How can I analyze these images? Is it a correct procedure to conform the
voxels using "mri_convert". Is this procedure correct? does it hurt the
anatomy of the images?
 
I highly appreciate your help
John
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Re: [Freesurfer] smoothing data

[Matt Glasser]

Smoothing in the volume is the single worst thing that is traditionally
done to brain imaging data as far as precision of spatial localization
goes.  

Peace,

Matt.

On 7/12/17, 5:46 PM, "Douglas N Greve"
 wrote:

>you should definitely not smooth the volume data. Smoothing should be
>limited to the surface.
>
>
>On 07/10/2017 11:33 AM, Tamara Tavares wrote:
>> Hi All,
>>
>> I was hoping someone can help me with two naive questions I have:
>>
>> I have read on the Freesufer wiki that you should smooth surface data
>> before analyzing. Should I smooth the data only after I have ran
>> recon-all and have made edits? Also, should volumetric data be
>> smoothed or is this limited to surface data?
>>
>> Thank you in advance for your help.
>>
>> Best,
>> Tamara
>>
>>
>> ___
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>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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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
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>properly
>dispose of the e-mail.
>


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Re: [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation

[Matt Glasser]

No.

From:   on behalf of "Tabassum,
Ruchira" 
Reply-To:  Freesurfer support list 
Date:  Saturday, August 5, 2017 at 12:22 PM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation

Hi,
 
I need Freesurfer for my windows OS. Is there any windows version of
FreeSurfer? Please let me know ASAP.
 
Kind Regards
Ruchira Tabassum
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Re: [Freesurfer] Brodmann areas - exvivo labels

[Matt Glasser]

I would use the versions where the group size approximately matched the
individual size.  

Peace,

Matt.

From:   on behalf of Trisanna
Sprung-Much 
Reply-To:  Freesurfer support list 
Date:  Tuesday, October 3, 2017 at 7:36 PM
To:  Freesurfer support list 
Subject:  [Freesurfer] Brodmann areas - exvivo labels

Hi there

If I wanted to compare some spatial probability maps of some sulci of
interest with the Juelich Data provided by FreeSurfer, would it make more
sense to use the unthresholded Brodmann areas or the .thresh ones? Based on
my understanding of how the .thresh was created (by creating a surface area
of the average BA label that best resembled the average surface area of the
label from each individual hemisphere) in order to avoid including vertices
that had a probability of 10%, for instance, I think using .thresh would be
fine. However, I thought I would verify. In input would be greatly
appreciated.


Best
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


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Re: [Freesurfer] Transformation between spaces

[Matt Glasser]

I¹d note that you can run the group ICA on surface data in surface space
pretty easily using melodic, which would avoid the issue that Doug mentions.

Peace,

Matt.

From:   on behalf of Douglas Greve

Reply-To:  Freesurfer support list 
Date:  Monday, October 9, 2017 at 7:20 PM
To:  
Subject:  Re: [Freesurfer] Transformation between spaces


 


 
 

How did you get your ICA analysis into MNI305 (or MNI152) space?  You're ICA
intergroup comparisons will only be as good as that space -- how you get it
onto the surface from there is not so important. You can run recon-all on
the MNI152, sample the ICA maps onto the surface, then use the surface-based
registration to map it to fsaverage.
 
 
 
On 10/9/17 7:20 PM, Florence Campana wrote:
 
 
>  
> Dear freesurfer experts,
> 
>  
>  
> I ran a spatial ICA in volume and would like to visualize the components in
> surface in order to assess the overlap between the  independent components and
> my ROI (defined on surface). However after reading this paper,
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am  concerned with
> transformations between the MNI 305 space and the surface space without
> totally understanding the nature of the distortions unfortunately. Would you
> mind explaining it briefly to me and let me know whether you think that the
> transformation of the components from the MNI305 space to the surface will
> lead to distorted results in the case of our spatial overlap estimates? (in
> which case I can define the ROI in volume and conduct all the analyses in
> volume).
>  
> 
>  
>  
> Thank you very much,
>  
> Florence Campana
>  
>  
>   
>  
> ___
> Freesurfer mailing list
> freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinf
> o/freesurfer
>  
 
 
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Re: [Freesurfer] Transformation between spaces

[Matt Glasser]

The latest version of melodic is compatible with CIFTI data (e.g. From the
HCP).

Peace,

Matt.

From:   on behalf of Florence
Campana 
Reply-To:  Freesurfer support list 
Date:  Monday, October 9, 2017 at 9:25 PM
To:  Freesurfer support list 
Subject:  [Freesurfer] Transformation between spaces

Hi Matt,

Thank you for your quick input ; I did not try yet to use melodic, it seems
indeed to be the most straightforward solution, I will try it, thank you
again!

Florence

Le lundi 9 octobre 2017, Matt Glasser  > a écrit :
> I¹d note that you can run the group ICA on surface data in surface space
> pretty easily using melodic, which would avoid the issue that Doug mentions.
> 
> Peace,
> 
> Matt.
> 
> From:   on behalf of Douglas Greve
> 
> Reply-To:  Freesurfer support list 
> Date:  Monday, October 9, 2017 at 7:20 PM
> To:  
> Subject:  Re: [Freesurfer] Transformation between spaces
> 
> 
>  
> 
> 
>  
>  
> 
> How did you get your ICA analysis into MNI305 (or MNI152) space?  You're ICA
> intergroup comparisons will only be as good as that space -- how you get it
> onto the surface from there is not so important. You can run recon-all on the
> MNI152, sample the ICA maps onto the surface, then use the surface-based
> registration to map it to fsaverage.
>  
>  
>  
> On 10/9/17 7:20 PM, Florence Campana wrote:
>  
>  
>>  
>> Dear freesurfer experts,
>> 
>>  
>>  
>> I ran a spatial ICA in volume and would like to visualize the components in
>> surface in order to assess the overlap between the  independent components
>> and my ROI (defined on surface). However after reading this paper,
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am  concerned with
>> transformations between the MNI 305 space and the surface space without
>> totally understanding the nature of the distortions unfortunately. Would you
>> mind explaining it briefly to me and let me know whether you think that the
>> transformation of the components from the MNI305 space to the surface will
>> lead to distorted results in the case of our spatial overlap estimates? (in
>> which case I can define the ROI in volume and conduct all the analyses in
>> volume).
>>  
>> 
>>  
>>  
>> Thank you very much,
>>  
>> Florence Campana
>>  
>>  
>>   
>>  
>> ___
>> Freesurfer mailing list
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>> fo/freesurfer
>>  
>  
>  
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Re: [Freesurfer] Transformation between spaces

[Matt Glasser]

You would be running melodic from the command line.  If you have further
questions on CIFTI, the better place to ask would be the HCP-Users mailing
list:

https://www.humanconnectome.org/contact-us

Peace,

Matt.

From:   on behalf of Florence
Campana 
Reply-To:  Freesurfer support list 
Date:  Tuesday, October 10, 2017 at 12:12 PM
To:  Freesurfer support list 
Subject:  Re: [Freesurfer] Transformation between spaces

Hi Matt,

I follow-up on your suggestion of running MELODIC in surface. I am unsure
about the registration files that I should use (I guess that they should be
surface files?), notably for the Main Structural Images and the Standard
Space.
I am sorry if this sounds like a naive question.

Thank you very much,

Florence

2017-10-09 22:28 GMT-04:00 Matt Glasser :
> The latest version of melodic is compatible with CIFTI data (e.g. From the
> HCP).
> 
> Peace,
> 
> Matt.
> 
> From:   on behalf of Florence  Campana
> 
> Reply-To:  Freesurfer support list 
> Date:  Monday, October 9, 2017 at 9:25 PM
> To:  Freesurfer support list 
> Subject:  [Freesurfer] Transformation between spaces
> 
> Hi Matt,
> 
> Thank you for your quick input ; I did not try yet to use melodic, it seems
> indeed to be the most straightforward solution, I will try it, thank you
> again!
> 
> Florence
> 
> Le lundi 9 octobre 2017, Matt Glasser  a écrit :
>> I¹d note that you can run the group ICA on surface data in surface space
>> pretty easily using melodic, which would avoid the issue that Doug mentions.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From:   on behalf of Douglas Greve
>> 
>> Reply-To:  Freesurfer support list 
>> Date:  Monday, October 9, 2017 at 7:20 PM
>> To:  
>> Subject:  Re: [Freesurfer] Transformation between spaces
>> 
>> 
>>  
>> 
>> 
>>  
>>  
>> 
>> How did you get your ICA analysis into MNI305 (or MNI152) space?  You're ICA
>> intergroup comparisons will only be as good as that space -- how you get it
>> onto the surface from there is not so important. You can run recon-all on the
>> MNI152, sample the ICA maps onto the surface, then use the surface-based
>> registration to map it to fsaverage.
>>  
>>  
>>  
>> On 10/9/17 7:20 PM, Florence Campana wrote:
>>  
>>  
>>>  
>>> Dear freesurfer experts,
>>> 
>>>  
>>>  
>>> I ran a spatial ICA in volume and would like to visualize the components in
>>> surface in order to assess the overlap between the  independent components
>>> and my ROI (defined on surface). However after reading this paper,
>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am  concerned with
>>> transformations between the MNI 305 space and the surface space without
>>> totally understanding the nature of the distortions unfortunately. Would you
>>> mind explaining it briefly to me and let me know whether you think that the
>>> transformation of the components from the MNI305 space to the surface will
>>> lead to distorted results in the case of our spatial overlap estimates? (in
>>> which case I can define the ROI in volume and conduct all the analyses in
>>> volume).
>>>  
>>> 
>>>  
>>>  
>>> Thank you very much,
>>>  
>>> Florence Campana
>>>  
>>>  
>>>   
>>>  
>>> ___
>>> Freesurfer mailing list
>>> freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listi
>>> nfo/freesurfer
>>>  
>>  
>>  
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>> 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
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> Compliance

Re: [Freesurfer] volume vs surface-based and surface smoothing

[Matt Glasser]

Volume-based registration is fine with subject as you have the same brain
that you are registering (ideally such registrations are 6 DOF rigid
registrations and any image distortions are corrected for).  Surface-based
registration is better when comparing across subjects due to the variability
in cortical folding patterns and locations of areas relative to folds across
subjects.  Smoothing is best done on the surface if it is done at all.
Smoothing in the volume harms one¹s spatial localization precision much more
than smoothing on the surface for an equivalent FWMH in mm.  It is worth
keeping in mind that smoothing on the surface does still blur across
cortical areal boundaries, however, so for many analyses it may be better to
average within cortical areas rather than to smooth a lot.

Peace,

Matt.

From:   on behalf of Alissa Stafford

Reply-To:  Freesurfer support list 
Date:  Thursday, October 12, 2017 at 12:29 PM
To:  "Freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] volume vs surface-based and surface smoothing

Hello,

I am trying to understand the preprocessing functions to successfully
complete surface-based analysis. I am confused about what is happening on
the volume level and when exactly the surface is being created. My questions
revolve around register-sess and rawfunc2surf-sess.

Registration has 2 parts:
1: the native anatomical space is registered with the fsaverage space. This
is happening during recon-all.
2: native functional data is registered with the native anatomical data.
This is happening during register-sess in preprocess-sess.
Aren¹t these both volume-based registrations? If not when are the surfaces
created? My concern is that it is volume-based and I was under the
impression from this article:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all
registrations should be done on the surface.

I am also confused about rawfunc2surf-sess. I believe up until this function
in preprocess-sess, everything has been done in the volume so this is the
first step that is done in the surface, is that correct? And then does this
do smoothing? I realized it has a fwhm input option so it must smooth. So is
this where the functional data is now expressed in the surface and it also
smooths? Or does surfsmooth-sess need to be run in addition to
rawfunc2surf-sess?

I basically just want to be making sure I understand when registration is
volume-based or surface-based and when it¹s appropriate to use volume-based.
And I was using the rawfunc2surf function assuming it was for smoothing, but
I am not so sure if this only creates the surface or also smooths.

Thanks,
Alissa
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Re: [Freesurfer] volume vs surface-based and surface smoothing

[Matt Glasser]

My understanding of the FreeSurfer surface-based functional processing is
that it adheres to the below guidelines; however, I have not personally used
it so we¹ll have to see what the FreeSurfer experts say.

Peace,

Matt.

From:   on behalf of Alissa Stafford

Reply-To:  Freesurfer support list 
Date:  Thursday, October 12, 2017 at 12:42 PM
To:  Freesurfer support list 
Subject:  Re: [Freesurfer] volume vs surface-based and surface smoothing

Thanks Matt! Does rawfunc2surf-sess create the surface and smooth?

From:  on behalf of Matt Glasser

Reply-To: Freesurfer support list 
Date: Thursday, October 12, 2017 at 1:39 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] volume vs surface-based and surface smoothing

Volume-based registration is fine with subject as you have the same brain
that you are registering (ideally such registrations are 6 DOF rigid
registrations and any image distortions are corrected for).  Surface-based
registration is better when comparing across subjects due to the variability
in cortical folding patterns and locations of areas relative to folds across
subjects.  Smoothing is best done on the surface if it is done at all.
Smoothing in the volume harms one¹s spatial localization precision much more
than smoothing on the surface for an equivalent FWMH in mm.  It is worth
keeping in mind that smoothing on the surface does still blur across
cortical areal boundaries, however, so for many analyses it may be better to
average within cortical areas rather than to smooth a lot.

Peace,

Matt.

From:  on behalf of Alissa Stafford

Reply-To: Freesurfer support list 
Date: Thursday, October 12, 2017 at 12:29 PM
To: "Freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] volume vs surface-based and surface smoothing

Hello,

I am trying to understand the preprocessing functions to successfully
complete surface-based analysis. I am confused about what is happening on
the volume level and when exactly the surface is being created. My questions
revolve around register-sess and rawfunc2surf-sess.

Registration has 2 parts:
1: the native anatomical space is registered with the fsaverage space. This
is happening during recon-all.
2: native functional data is registered with the native anatomical data.
This is happening during register-sess in preprocess-sess.
Aren¹t these both volume-based registrations? If not when are the surfaces
created? My concern is that it is volume-based and I was under the
impression from this article:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all
registrations should be done on the surface.

I am also confused about rawfunc2surf-sess. I believe up until this function
in preprocess-sess, everything has been done in the volume so this is the
first step that is done in the surface, is that correct? And then does this
do smoothing? I realized it has a fwhm input option so it must smooth. So is
this where the functional data is now expressed in the surface and it also
smooths? Or does surfsmooth-sess need to be run in addition to
rawfunc2surf-sess?

I basically just want to be making sure I understand when registration is
volume-based or surface-based and when it¹s appropriate to use volume-based.
And I was using the rawfunc2surf function assuming it was for smoothing, but
I am not so sure if this only creates the surface or also smooths.

Thanks,
Alissa
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] asking for literature

[Matt Glasser]

Also we used T2w scans in the HCP Pipelines Paper and have Figure 14
showing the effects of using T2w scan vs not using one.

Peace,

Matt.

On 10/20/17, 10:00 AM, "Bruce Fischl"
 wrote:

>Hi Jiook
>
>this paper:
>
>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/
>
>discusses the basic algorithm (it is based on T2* but is pretty much the
>same for T2)
>
>cheers
>Bruce
>On Fri, 20 Oct 2017,
>Jiook Cha wrote:
>
>> Hello,
>> 
>> Could anybody please point me to a paper/asbtract showing meaningful
>>improvement of pial surface
>> segmentation using additional T2 or Flair images in the recon-all
>>procedure?
>> 
>> 
>> Thanks,
>> 
>> Jiook
>> 
>>[t?sender=aY2hhLmppb29rQGdtYWlsLmNvbQ%3D%3D&type=zerocontent&guid=4aae682
>>8-1e3e-430a-9278-8ede4ceeb
>> f60] ᐧ
>> 
>>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>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] bbregister error -- Human Connectome Project Data

[Matt Glasser]

You would be better off resampling the existing CIFTI data to the fsaverage4
surface rather than redoing the projection and smoothing in the volume.
Instructions for getting to fsaverage are available here:

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

Also I would recommend starting from the ICA+FIX cleaned data, not the
minimally preprocessed data.  If you must smooth the data, you can do that
with wb_command -cifti-smoothing before following the above steps.

Peace,

Matt.

From:   on behalf of Lana Ruck

Reply-To:  Freesurfer support list 
Date:  Wednesday, December 27, 2017 at 4:41 PM
To:  
Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data

As a work-around to the above issue, I did the registrations directly in FSL
using FLIRT, and then converted the resultant fsl reg.mat files to
freesurfer reg.dat files (using tkregister2; they all look fine). Now, all I
need is to project these rfMRI data to fsaverage4, and I thought
mri_vol2surf was the right way to do this.

Unfortunately, I am now having the same directory issue with mri_vol2surf
(new error log below), where it can't find /surf/lh.white for my subject.
The HCP pre-processed data has already been through recon-all, so there are
several *white*surf* files to choose from for each subject, but they are not
in the directory specified by default in MRISread (subjid/surf/).

I thought I could fix this by specifying the right target subject
(--trgsubject fsaverage4, which I have manually copied, along with the other
$FREESURFER_HOME/subjects, to my own $SUBJECTS_DIR as per the message
boards), or specifying the right directory (I've tried the --surf command
with both the fsaverage4 path, and to multiple [subject]?h.white paths, but
it just appends them to the non-existent default path--see below). Thus,
regardless of what I specify, I keep getting the same error related to a
default search in subjid/surf/.

Is there a way to point MRISread to the correct surf files, without re-doing
recon-all or moving the pre-processed surfaces to a "surf" folder for all 40
subjects?

Lana

> [lruck@c5 LH_all]$ mri_vol2surf --mov
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> .img --src_type analyze --reg
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> _register.dat --hemi lh --fwhm 6 --trgsubject fsaverage4 --surf
> /N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white --out
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/
> srcvol = 
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> .img
> srctype = analyze
> srcreg = 
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> _register.dat
> srcregold = 0
> srcwarp unspecified
> surf = /N/dc2/scratch/lruck/LEH_all/fsaverage4/surf/lh.white
> hemi = lh
> trgsubject = fsaverage4
> surfreg = sphere.reg
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
>   analyzeRead() roi_scale   0.0
> Done loading volume
> INFO: This REGISTER_DAT transform is valid only for volumes between  COR types
> with c_(r,a,s) = 0.
> Input reg is register.dat
>  original matrix ---
>  0.96607   0.00120   0.00047  -0.78994;
>  0.01685   0.96915  -0.00899   2.16005;
> -0.00580  -0.00642   0.98726  -0.56166;
>  0.0   0.0   0.0   1.0;
>  original matrix ---
> INFO: smoothing volume at fwhm = 6 mm (std = 2.54797)
> Reading surface 
> /N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaver
> age4/surf/lh.white
> MRISread(/N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_a
> ll/fsaverage4/surf/lh.white): could not open file
> No such file or directory
> mri_vol2surf: could not read surface
> /N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaver
> age4/surf/lh.white
> No such file or directory


   
Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 1:43 PM, Lana Ruck  wrote:
> Hello, 
> 
> I am currently starting a project with the minimally pre-processed rfMRI from
> the Human Connectome Project, but I need to do some additional processing
> first. This includes smoothing at 6mm FWHM and projection onto the fsaverage4
> surface. I have smoothed the pre-processed rfMRI data using mri_convert (and
> have also converted the provided brain-extracted anatomical), but I am having
> issues registering the smoothed rfMRI volumes, and I understand that I need
> these register.dat files for mri_vol2surf.
> 
> I have tried bbregister --init-fsl; bbregister --init-spm; and manual
> registration using tkregister2. All of them give me the same error--I think it
> is a pat

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Matt Glasser]

I wouldn¹t trust resting state data that have not been properly denoised.
You should only need the structural and FIX cleaned packages for what you
are doing.  The link that I put below explains how to get HCP data onto the
fsaverage4 surface.  You will need FreeSurfer and Connectome Workbench for
this.  

Peace,

Matt.

From:   on behalf of Lana Ruck

Reply-To:  Freesurfer support list 
Date:  Wednesday, December 27, 2017 at 5:55 PM
To:  Freesurfer support list 
Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data

Matt,

Thanks for the quick reply! I'll check out that Wiki document and the 2016
Nature paper first.

The reason I have the pre-processed (but not ICA-FIX'ed) rfMRI data is
because I would like to use the iterative parcellation algorithm from the
Liu Lab @Harvard (as described in Wang, D. et al. 2015: Parcellating
Cortical Functional Networks in Individuals. Nat. Neurosci;
http://nmr.mgh.harvard.edu/bid/DownLoad.html), but I am unsure if the
ICA-FIX data are appropriate for this. I know that the minimally
pre-processed rfMRI data just need to be smoothed and projected to
fsaverage4 for the MATLAB algorithm to work, but I didn't see a clear way to
get the ICA-FIX data in the right format, as per the specifications provided
by the Lui Lab. I am also not using a local machine to do the processing (I
am using my Uni's supercomputing infrastructure), so I don't know if I can
get connectome workbench installed in order to pre-process CIFTI data.
That's why I am working with standard formats (the supercomputer has
freesurfer, fsl, etc.).

Assuming I can get cnm-wb installed by admins on the supercomputer, and that
I can use it to get the ICA-FIX data appropriately formatted for
parcellation with MATLAB, do you suggest I download the extended packages,
or will the compact ones have everything I need?

Lana

   
Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 6:26 PM, Matt Glasser  wrote:
> You would be better off resampling the existing CIFTI data to the fsaverage4
> surface rather than redoing the projection and smoothing in the volume.
> Instructions for getting to fsaverage are available here:
> 
> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-
> 9.HowdoImapdatabetweenFreeSurferandHCP?
> 
> Also I would recommend starting from the ICA+FIX cleaned data, not the
> minimally preprocessed data.  If you must smooth the data, you can do that
> with wb_command -cifti-smoothing before following the above steps.
> 
> Peace,
> 
> Matt.
> 
> From:   on behalf of Lana Ruck
> 
> Reply-To:  Freesurfer support list 
> Date:  Wednesday, December 27, 2017 at 4:41 PM
> To:  
> Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data
> 
> As a work-around to the above issue, I did the registrations directly in FSL
> using FLIRT, and then converted the resultant fsl reg.mat files to freesurfer
> reg.dat files (using tkregister2; they all look fine). Now, all I need is to
> project these rfMRI data to fsaverage4, and I thought mri_vol2surf was the
> right way to do this.
> 
> Unfortunately, I am now having the same directory issue with mri_vol2surf (new
> error log below), where it can't find /surf/lh.white for my subject. The HCP
> pre-processed data has already been through recon-all, so there are several
> *white*surf* files to choose from for each subject, but they are not in the
> directory specified by default in MRISread (subjid/surf/).
> 
> I thought I could fix this by specifying the right target subject
> (--trgsubject fsaverage4, which I have manually copied, along with the other
> $FREESURFER_HOME/subjects, to my own $SUBJECTS_DIR as per the message boards),
> or specifying the right directory (I've tried the --surf command with both the
> fsaverage4 path, and to multiple [subject]?h.white paths, but it just appends
> them to the non-existent default path--see below). Thus, regardless of what I
> specify, I keep getting the same error related to a default search in
> subjid/surf/.
> 
> Is there a way to point MRISread to the correct surf files, without re-doing
> recon-all or moving the pre-processed surfaces to a "surf" folder for all 40
> subjects?
> 
> Lana
> 
>> [lruck@c5 LH_all]$ mri_vol2surf --mov
>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1L
>> R.img --src_type analyze --reg
>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1L
>> R_register.dat --hemi lh --fwhm 6 --trgsubject fsaverage4 --surf
>> /N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white --

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Matt Glasser]

There is a structural extended package that has the FreeSurfer folders.

Peace,

Matt.

From:   on behalf of Lana Ruck

Reply-To:  Freesurfer support list 
Date:  Thursday, December 28, 2017 at 12:56 PM
To:  Freesurfer support list 
Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data

Okay so if I am going to try and run this option, recon-all must also be
done on the structural scans. I have the pre-processed structurals, and I
understand from y'all's 2013 paper
<http://linkinghub.elsevier.com/retrieve/pii/S1053811913005053>  that they
have already been through all of the steps in recon-all. First--is it
correct that all steps (1-31) have been done on the data? Second, as with my
original question, it seems that the HCP directories are quite different
than the defaults that would be created by a standard Freesurfer recon-all
run. Assuming that Freesurfer scripts will look for recon-all files in
directories not present in the HCP data as downloaded, (for example,
subjid/mri/... and subj/surf/... are not valid paths in the pre-processed
data), would it just be better to get the un-processed structurals and
re-run all of the recon-all steps myself?

I guess I'm just wondering what the value of the pre-processed data is if it
is re-organized as to be un-readable by Freesurfer defaults.

Lana

   
Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 7:02 PM, Matt Glasser  wrote:
> I wouldn¹t trust resting state data that have not been properly denoised.  You
> should only need the structural and FIX cleaned packages for what you are
> doing.  The link that I put below explains how to get HCP data onto the
> fsaverage4 surface.  You will need FreeSurfer and Connectome Workbench for
> this.  
> 
> Peace,
> 
> Matt.
> 
> From:   on behalf of Lana Ruck
> 
> Reply-To:  Freesurfer support list 
> Date:  Wednesday, December 27, 2017 at 5:55 PM
> To:  Freesurfer support list 
> 
> Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data
> 
> Matt,
> 
> Thanks for the quick reply! I'll check out that Wiki document and the 2016
> Nature paper first.
> 
> The reason I have the pre-processed (but not ICA-FIX'ed) rfMRI data is because
> I would like to use the iterative parcellation algorithm from the Liu Lab
> @Harvard (as described in Wang, D. et al. 2015: Parcellating Cortical
> Functional Networks in Individuals. Nat. Neurosci;
> http://nmr.mgh.harvard.edu/bid/DownLoad.html), but I am unsure if the ICA-FIX
> data are appropriate for this. I know that the minimally pre-processed rfMRI
> data just need to be smoothed and projected to fsaverage4 for the MATLAB
> algorithm to work, but I didn't see a clear way to get the ICA-FIX data in the
> right format, as per the specifications provided by the Lui Lab. I am also not
> using a local machine to do the processing (I am using my Uni's supercomputing
> infrastructure), so I don't know if I can get connectome workbench installed
> in order to pre-process CIFTI data. That's why I am working with standard
> formats (the supercomputer has freesurfer, fsl, etc.).
> 
> Assuming I can get cnm-wb installed by admins on the supercomputer, and that I
> can use it to get the ICA-FIX data appropriately formatted for parcellation
> with MATLAB, do you suggest I download the extended packages, or will the
> compact ones have everything I need?
> 
> Lana
> 
>  
> Lana Ruck, M.A.
> Associate Instructor, Department of Anthropology
> Graduate Scholars Fellow, Cognitive Science Program
> Indiana University, Bloomington
> Student Building 166
> lr...@umail.iu.edu
> 
> 
> On Wed, Dec 27, 2017 at 6:26 PM, Matt Glasser  wrote:
>> You would be better off resampling the existing CIFTI data to the fsaverage4
>> surface rather than redoing the projection and smoothing in the volume.
>> Instructions for getting to fsaverage are available here:
>> 
>> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ
>> -9.HowdoImapdatabetweenFreeSurferandHCP?
>> 
>> Also I would recommend starting from the ICA+FIX cleaned data, not the
>> minimally preprocessed data.  If you must smooth the data, you can do that
>> with wb_command -cifti-smoothing before following the above steps.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From:   on behalf of Lana Ruck
>> 
>> Reply-To:  Freesurfer support list 
>> Date:  Wednesday, December 27, 2017 at 4:41 PM
>> To:  
>> Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data

Re: [Freesurfer] recommendation for T1 and T2-based sequences use with FreeSurfer

[Matt Glasser]

I think the HCP CCF protocol is a good start:

http://protocols.humanconnectome.org/

Peace,

Matt.

From:   on behalf of Colm Connolly

Reply-To:  Freesurfer support list 
Date:  Tuesday, February 6, 2018 at 10:41 AM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] recommendation for T1 and T2-based sequences use with
FreeSurfer

Hi everybody, 

I¹m endeavoring to help a researcher come up with a protocol which might be
³optimal² (in some sense) for use with FreeSurfer. I¹ve not really used
FreeSurfer much hence my lack of familiarity with what the recommended
sequences are for use with FreeSurfer.

Having searched around, I¹ve found [1]. Do the recommendations in [1] still
apply?

I¹d like the researcher to get good pial surface estimate so would like to
be able to recommend that he perform a T2 scan as well. Having read through
[2], it makes mention of T2 and FLAIR images for improving pial surface
estimation. Is the FLASH image recommended in [1] appropriate for use with
the -T2 or -FLAIR args to recon-all?

We¹ll be running these scans on a 3T Siemens Prisma running V11c software.
Are there particular scans that you recommend for this particular scanner or
again does [1] apply?

[1] 
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&d
o=get&target=FreeSurfer_Suggested_Morphometry_Protocols.pdf
[2] 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimpr
ovepialsurfaces

Thanks in advance for you time,

Regards,
--
Colm G. Connolly, PhD
Dept of Biomedical Sciences
Florida State University
Tallahassee, FL 32306
Tel: +1-850-644-2105
https://www.researchgate.net/profile/Colm_Connolly2

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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

[Matt Glasser]

I don’t know if recon-all will pass those flags in or not.  Probably best
to let Bruce take a look.

Peace,

Matt.

On 5/13/14, 7:36 AM, "Bruce Fischl"  wrote:

>Hi Emil
>
>I would need the entire subject dir plus the T2-space volume
>
>cheers
>Bruce
>On Tue, 13 May 
>2014, Emil H.J. Nijhuis wrote:
>
>> 
>> Dear Bruce & Matt,
>> thank you for your help.
>> 
>> @Bruce: I would be happy to send you the data, just let me know by
>>e-mail which files you wo
>> uld need.
>> 
>> @Matt: Could you please specify the commands for the flags
>>-nsigma_above and -nsigma_below a
>> nd how you would rerun the pipeline? Also what values would be
>>recommended?
>> 
>> I did not find any manual/help files regarding the flags, so it would
>>be helpful to document
>>  it.
>> 
>> NB. I found another thread in the maillist which probably relates to
>>the issue: https://mail
>> .nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033550.html .
>>However I could not
>> verify this, due to expired dropbox files.
>> 
>> Yours,
>>
>>  Emil
>> 
>> Probably Emil¹s current example would be best because it is failing in
>> your recon-all setup.
>> 
>> Matt.
>> 
>> On 5/9/14, 9:31 AM, "Bruce Fischl"  wrote:
>> 
>> >Hi Matt
>> >
>> >if you can send me an example I'll try to find time to take a look
>> >Bruce
>> >On Fri, 9 
>> >May 2014, Matt Glasser wrote:
>> >
>> >> Hi Bruce,
>> >> 
>> >> For whatever reason, sometimes the T2w surface adjustment will be way
>> >>off.
>> >>  Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit
>>up
>> >>and
>> >> down can get it out of the minimum and make it work, so there might
>>be a
>> >> bug. 
>> >> 
>> >> Peace,
>> >> 
>> >> Matt.
>> >> 
>> >> From: "Emil H.J. Nijhuis" 
>> >> Reply-To: Freesurfer support list 
>> >> Date: Friday, May 9, 2014 at 4:53 AM
>> >> To: 
>> >> Subject: Re: [Freesurfer] problem with pial surface reconstruction
>> >>using T1
>> >> (MPRAGE) and T2 (SPACE) weighted images
>> >> 
>> >> Dear Bruce,
>> >> 
>> >> thank you for your help.
>> >> 
>> >> attached I have put an fslview, tkmedit screen-shot of the T2 image
>>and
>> >>a tk
>> >> surfer image of lh.woT2.pial.
>> >> 
>> >> It appears that without consideration of the T2 this effect does not
>> >>happen.
>> >> 
>> >> What would be your recommendation if I would like to keep using the
>>T2
>> >>weigh
>> >> ted image?
>> >> 
>> >> Yours,
>> >>  Emil
>> >> 
>> >> Hi Emil
>> >> 
>> >> how do the surfaces look before you apply the T2 deformation? And
>>how do
>> >> they look visualized over the T2 instead of the T1?
>> >> 
>> >> cheers
>> >> Bruce
>> >> 
>> >> On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
>> >> 
>> >> Hi,
>> >> 
>> >> I have been using Freesurfer v5.3 to perform surface reconstruct for
>>1mm
>> >> isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens
>>3T
>> >>Trio
>> >> scanner with a 32-channel head coil. Unfortunately for half of my
>> >>subjects I
>> >> receive an rather odd pial surface artefact, while the 'white'
>>surfaces
>> >>do
>> >> not suffer from the same issue.
>> >> 
>> >> The command line I have used was:
>> >> 
>> >> recon-all -all -subjid  -T2  /mri/orig/T2.mgz
>> >>-T2pial
>> >> -3T
>> >> 
>> >> Are you familiar with this issue and do you have some advice for me?
>> >> 
>> >> Thank you very much for your help.
>> >> 
>> >> Yours sincerely,
>> >> 
>> >>  Emil
>> >> 
>> >> --
>> >> --
>> >> Emil H.J. Nijhuis, PhD
>> >> Researcher - Division of Diagnostic and Interventional Neuroradiology
>> >> University Hospital Basel
>> >> Petersgraben 4
>> >> CH 4031 B

Re: [Freesurfer] mris_convert to GIFTI misaligned in freeview

[Matt Glasser]

Yes the HCP pipelines have to take care of this as well so that the
surfaces and volume align outside of FreeSurfer.

Peace,

Matt.

On 5/27/14, 8:35 AM, "Franz Liem"  wrote:

>Hi Michael,
>
>I had a similar problem a while ago. Maybe this might help.
>http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31152.html
>
>Best,
>Franz
>
>Am 23.05.2014 um 05:38 schrieb Harms, Michael:
>
>> 
>> Hi,
>> I converted a surface to GIFTI
>> e.g.,
>> mris_convert lh.white lh.white.gii
>> 
>> lh.white and lh.white.gii align when they are both loaded in 'tkmedit'.
>> However, they do not align when loaded simultaneously in 'freeview'.
>> 
>> Of possible relevance: When I loaded lh.white.gii into 'freeview', I
>>got the following message in the terminal:
>> "Did not find any volume geometry information in the surface"
>> 
>> Is this possibly a bug of some sort in the display of GIFTI surfaces
>>within 'freeview'?
>> 
>> This was all done with FS 5.3.
>> 
>> thanks,
>> -MH
>> 
>> -- 
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave.  Tel: 314-747-6173
>> St. Louis, MO  63110  Email: mha...@wustl.edu
>> 
>>  
>> 
>> 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
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Re: [Freesurfer] Convert label file to STL file‏

[Matt Glasser]

It probably thinks the STL file is just a mesh without coloring.

Peace,

Matt.

From:  Mat yuki 
Reply-To:  Freesurfer support list 
Date:  Thursday, July 10, 2014 at 7:19 AM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Convert label file to STL file‏

Dear Freesurfer Experts,
 
I'm trying to convert .label file to .stl file.
In more detail of my purpose, I want to get separate stl files of whole
brain. 
Now, I want to make stl files of label files which made from
?h.aparc.a2009s.annot.
 
First, I tried to convert lh.pial to lh.pial.stl, I've got it (this was just
check how mris_convert works).
Second, I copied lh. white file from surf dir into label dir. Then, I runed
next command:
 
cd /label
mris_convert --label lh.bankssts.label bankssts lh.white
lh.bankssts.label.stl
 
And got the error message: ERROR: unknown file annot file type specified for
output: lh.bankssts.label.stl
 
Do you know what could have gone wrong?

Thank you,
Yuki.   
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Re: [Freesurfer] T2-space vs T2-space-FLAIR

[Matt Glasser]

Bruce has said the FLAIR might be a little better for FreeSurfer but it¹s
worse for myelin maps (has less CNR for the myelin, though you can still see
the major areas).  Currently, the T2 and FLAIR flags do exactly the same
thing, so it doesn¹t even matter what flag you use.  I think it depends on
what else you might want to do with the data (i.e. if myelin maps were
important to your study you might go with T2w (like HCP), but if lesion
detection were more important you might go with FLAIR (like biobank).

Peace,

Matt.

From:  Satrajit Ghosh 
Reply-To:  Freesurfer support list 
Date:  Wednesday, July 30, 2014 at 1:01 PM
To:  Freesurfer Mailing List 
Subject:  [Freesurfer] T2-space vs T2-space-FLAIR

hi bruce,

is there any difference from freesurfer's perspective of using T2-space or
T2-space-flair?

cheers,

satra

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Re: [Freesurfer] T2-space vs T2-space-FLAIR

[Matt Glasser]

Yes we performed both on the same subject in the same session and then
compared the myelin map results.

Peace,

Matt.

From:  Satrajit Ghosh 
Reply-To:  Freesurfer support list 
Date:  Wednesday, July 30, 2014 at 1:53 PM
To:  Freesurfer support list 
Subject:  Re: [Freesurfer] T2-space vs T2-space-FLAIR

thanks matt,

would like to be sure that your comments in relation to the T2-space-flair
sequence and not the typical clinical TSE-FLAIR. is that the case?

cheers,

satra


On Wed, Jul 30, 2014 at 2:23 PM, Matt Glasser  wrote:
> Bruce has said the FLAIR might be a little better for FreeSurfer but it¹s
> worse for myelin maps (has less CNR for the myelin, though you can still see
> the major areas).  Currently, the T2 and FLAIR flags do exactly the same
> thing, so it doesn¹t even matter what flag you use.  I think it depends on
> what else you might want to do with the data (i.e. if myelin maps were
> important to your study you might go with T2w (like HCP), but if lesion
> detection were more important you might go with FLAIR (like biobank).
> 
> Peace,
> 
> Matt.
> 
> From:  Satrajit Ghosh 
> Reply-To:  Freesurfer support list 
> Date:  Wednesday, July 30, 2014 at 1:01 PM
> To:  Freesurfer Mailing List 
> Subject:  [Freesurfer] T2-space vs T2-space-FLAIR
> 
> hi bruce,
> 
> is there any difference from freesurfer's perspective of using T2-space or
> T2-space-flair?
> 
> cheers,
> 
> satra
> 
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Re: [Freesurfer] Left and Right Vessels

[Matt Glasser]

I believe their function is to carry blood from one place to another.

Peace,

Matt.

From:  Mohammed Goryawala 
Reply-To:  Freesurfer support list 
Date:  Tuesday, August 19, 2014 at 1:55 PM
To:  "Freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Left and Right Vessels

Hello Freesurfer experts,

In a study I found significant differences in the volume of the left and
right vessels of the freesurfer atlas.

I wanted to know what regions are included in that ROI and if there are any
known functions of these regions.

Thank you

Mohammed Goryawala, PhD
Miller School of Medicine,
University of Miami
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Re: [Freesurfer] Left and Right Vessels

[Matt Glasser]

Virchow­Robin spaces is another name for those (they are normal in small
amounts, not old strokes, and filled with CSF-like fluid).

Peace,

Matt.

On 8/21/14, 9:23 AM, "Bruce Fischl"  wrote:

>Hi Mohammed
>
>these are dark regions, usually in inferior pallidum/putamen. There
>intensity is different enough from gray matter that having it be a
>separate 
>class helps us label them more accurately. They could also be lacunae and
>not vessels.
>
>cheers
>Bruce
>
>
>On Tue, 19 Aug 2014, Mohammed Goryawala
>wrote:
>
>> Hello Freesurfer experts,
>> 
>> In a study I found significant differences in the volume of the left and
>> right vessels of the freesurfer atlas.
>> 
>> I wanted to know what regions are included in that ROI and if there are
>>any
>> known functions of these regions.
>> 
>> Thank you
>> 
>> Mohammed Goryawala, PhD
>> Miller School of Medicine,
>> University of Miami
>> 
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Re: [Freesurfer] how to shrink wm surface

[Matt Glasser]

Have a look at mris_make_surfaces.c, this is how I learned about most of
this stuff as the code is pretty well commented (and Bruce telling me
things).

Peace,

Matt.

On 9/12/14, 11:01 PM, "Harms, Michael"  wrote:

>
>Hi Bruce,
>I was wondering if there is info somewhere about what each of those 7 MIN_
>and MAX_ variables control regarding the positioning of the white and pial
>surfaces?
>
>thanks,
>-MH
>
>--
>Michael Harms, Ph.D.
>
>---
>Conte Center for the Neuroscience of Mental Disorders
>Washington University School of Medicine
>Department of Psychiatry, Box 8134
>660 South Euclid Ave.   Tel: 314-747-6173
>St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
>On 9/9/14 7:35 AM, "Bruce Fischl"  wrote:
>
>>Hi Andrea
>>
>>what is the background image? This is usually either a failure of the
>>intensity normalization or of the surface deformation/segmentation to
>>adaptively estimate the underlying intensity distributions of the
>>gray/white matter. If you look in recon-all.log for that subject you will
>>find a set of lines like:
>>
>>setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70)
>>setting MAX_BORDER_WHITE to 112.0 (was 105)
>>setting MIN_BORDER_WHITE to 83.0 (was 85)
>>setting MAX_CSF to 59.1 (was 40)
>>setting MAX_GRAY to 100.0 (was 95)
>>setting MAX_GRAY_AT_CSF_BORDER to 77.0 (was 75)
>>setting MIN_GRAY_AT_CSF_BORDER to 47.2 (was 40)
>>
>>
>>
>>in your case for example you will probably find that the min_border_white
>>is too high or tha the max_gray is too low. You can set these using the
>>expert opts for both mri_segment and mris_make_surfaces.
>>
>>cheers
>>Bruce
>>
>>
>>On Tue, 9 Sep 2014, Andrea
>>Horváth wrote:
>>
>>> Dear Freesurfers,
>>>
>>>
>>> After running recon-all, the wm surfaces are too close to the pial
>>>surface,
>>> some gray matter is segmented as white matter as seen in the attached
>>> picture (red cross: a bigger cortical part is included in the white
>>>matter).
>>>
>>> How can I shrink the wm surface?
>>>
>>> Thank you for your help!
>>>
>>> Andrea
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>
>
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Re: [Freesurfer] Overclocking CPU for Freesurfer

[Matt Glasser]

It will just run faster so long as things like memtest86 and prime95 don¹t
have errors.

Peace,

Matt.

From:  "Chiu, Bryan (PHTH)" 
Reply-To:  Freesurfer support list 
Date:  Monday, September 29, 2014 at 4:26 PM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Overclocking CPU for Freesurfer

Hi, 

Is anyone aware of any issues that arise from overclocking and using
Freesurfer? I was looking to see how much it would speed up recon-all with
OpenMP using a stable overclock.

___
Bryan Chiu
Undergraduate Research Assistant
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy
Faculty of Medicine
University of British Columbia
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Re: [Freesurfer] Quality of surface-based alignment

[Matt Glasser]

What criteria would you use to determine one alignment was better than
another?

Peace,

Matt.

From:  "Caspar M. Schwiedrzik" 
Reply-To:  Freesurfer support list 
Date:  Tuesday, November 4, 2014 at 7:17 AM
To:  "Freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Quality of surface-based alignment

Hi Freesurfers, 
I was wondering whether there is a good way to assess post-hoc how well the
alignment between two surfaces was. I wouldn't like to run the alignment
again, but I could, if necessary. I would like to compare this alignment to
a bunch of other alignments to see whether it was worse than the others.
Thanks, Caspar

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Re: [Freesurfer] PySurfer - A package for visualizing surfaces

[Matt Glasser]

Hi Michael,

Out of curiosity, does this also support the GIFTI format?  If so, one could
use it to view surface data from a wide variety of software packages.

Thanks,

Matt.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael Waskom
Sent: Friday, July 22, 2011 1:07 PM
To: Freesurfer@nmr.mgh.harvard.edu
Cc: Alexandre Gramfort; Scott Burns
Subject: [Freesurfer] PySurfer - A package for visualizing surfaces

Dear Freesurfers,

We are pleased to announce the 0.1 release of PySurfer, a Python-based
package for the visualization of surface data from Freesurfer.  Please
see our website at http://pysurfer.github.com/ for information on how
to install the package and a gallery of examples.  We hope you'll find
it useful in your research!

Best,
Michael Waskom
Alexandre Gramfort
Scott Burns
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Re: [Freesurfer] Question about if there is constant number of vertexes across different brains

[Matt Glasser]

There are different numbers of vertices in subjects surfaces.  It is
possible to resample subjects' surfaces to a common mesh after registration,
but the FreeSurfer folks don't prefer this approach.  They prefer to simply
resample the quantitative data.  

Peace,

Matt.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Knut J Bjuland
Sent: Sunday, July 24, 2011 11:08 AM
To: Freesurfer Mailing List
Subject: [Freesurfer] Question about if there is constant number of vertexes
across different brains

Hi I have read (Dale, Fischl et al. 1999) and (Fischl, Sereno et al.
1999) . I have a question about if I understood the tessellation
procedure right. There are two vertexes in each voxel, but is the total
number of vertex constant across brains. I believe that number of total
vertex does not change over brain since it will be difficult to do
statically measure if the total numbers of vertex change. Nevertheless,
the shape and size of the vertex do change. Is this a correct assumption?

Knut J

Referanse liste

Dale, A. M., B. Fischl, et al. (1999). "Cortical surface-based analysis.
I. Segmentation and surface reconstruction." Neuroimage 9(2): 179-194.
Fischl, B., M. I. Sereno, et al. (1999). "Cortical surface-based
analysis. II: Inflation, flattening, and a surface-based coordinate
system." Neuroimage 9(2): 195-207.


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Re: [Freesurfer] label value 0 in annot file

[Matt Glasser]

Zero probably means "no label."

 

Peace,

 

Matt.

 

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Forrest Sheng
Bao
Sent: Sunday, July 31, 2011 3:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] label value 0 in annot file

 

hi,

I noticed an interesting thing today. I used read_annotation function in
matlab to load an .annot file, i.e.,
[Vertexes,Label,Colortable]=read_annotation(AnnotFile);

But some labels in Labels were 0's. They did not appear in the 5th column of
Colortable.table. And 0 was the only label that i couldn't find in the 5th
column of Colortable.table. All other labels were fine. 

Any idea what the cause of 0's as labels might be? 

Cheers, Forrest

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Re: [Freesurfer] Label2label on fsaverage

[Matt Glasser]

So I thought the issue had been solved, but perhaps not.  Bruce, we (i.e.
David) think the problem with Rouhi's data is that FreeSurfer did not detect
that the original images were tipped forward 90 degrees and as a result the
surface registration failed intermittently (i.e. in some subjects it okay,
but in others it is not).  These data were created with a fairly old version
of FreeSurfer (Rouhi can give the version number), and then a significant
amount of manual effort was put into defining some retinotopy on the data.
Therefore it isn't really a feasible option to just rerun the data with a
newer version of FreeSurfer, but we want to make use of accurate FreeSurfer
surface registration to make group average retinotopy results.  So the
question is how do we go about making sure the spheres are initialized to
have the correct rigid orientation before the registration proceeds.

 

Thanks,


Matt.

 

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Rouhollah
Abdollahi
Sent: Friday, August 12, 2011 12:38 PM
To: Bruce Fischl
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Label2label on fsaverage

 

I tried to rotate the surface by tksurfer and save it as new file . But when
I open the new surface like white it was not rotated.
Is there any special thing that I have to do?

Best 
Rouhi

On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi 
wrote:

Dear Bruce 
If I want to rotate sucli pattern too if it is the same? 


 

On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl 
wrote:

I guess you could rotate the surfaces, save them, then resample the labels
so that they get the new surface coords and sample them into the volume,
then onto the newly created surfaces. Not sure, we haven't ever had to do
anything like this.



On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:

Dear Bruce
I think the easiest way is to create all surfaces again but with corrected
and well aligned brain. The next step for me to create new labels from old
labels based on white surface (90 degree rotated) to new white surface. But
how? Is there any way to do that? I mean like label2label or surf2surf if
two surfaces are the same but one of them only rotated?!

Bests
Rouhi

On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl 
wrote:
 I don't see how anything would work if it was off by 90deg, but
 I guess you should try it



On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:

 Because I am using a result from a very old experiment
 that done on wrong direction and the  orig.mgz s   are not
 oriented according to
 freesurfer template. I cannot creat white because all
 results that I have (label files) are on white surface.
 The only way that I think I need to
 realign all surfaces and volume and apply that rotation on
 my label files.
  

 On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl
  wrote:
  not easily. Why would you need to do such a thing?


 On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:

  Dear Bruce

  I have a data set which I can not create the white
 surfaces because all of my results are according to white
 surface. I would
  like to know is
  there any way to rotate all surfaces and volumes and
 labels ... (everything) after finishing recon-all process.
 like 90 degree
  around  X axis? 
  and apply this rotation to all data set?

  Best
  Rouhi


  On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl
  wrote:
   Hi Rouhi

   I don't really understand. Are you saying you
 transformed the initial image before giving it to
 recon-all? There is a
  switch to
   mris_register to initialize with the tal xform,
 but we never use it as in pretty extensive tests it didn't
 seem to help.
   mris_register has a very large initial capture
 range due to it's global search, so I would be surprised
 if the initial
  orientation
   was the problem.

   cheers
   Bruce


   On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote:

   Dear Bruce
   I think I found the problem. The problem came
 from the original oriantation of T1 image and I think
 mris_register could
  not
   find it itself during
   the recon-all. I added to have initial alignment
 to inflated and the problem solved.( mris_register -curve
 -inflated 
   ?h.sphere?h.sphere.reg ) I think it is very
 important to add it to recon-all because if the user
 doesn't know the real
   oriantation it might make
   such a problem.

   Thanks for your quick response.

   On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah
 Abdollahi  wrote:
Dear Bruce

I am working on