[Freesurfer] Building your own fsaverage
Dear FreeSurfer team, I'm making a surface based group analysis of 40 multiple sclerosis subjects using FreeSurfer tools. What are the advantages of building your own fsaverage (make_average_subject) instead of using the premade fsaverage? Would you in general recommend this? What is the pro's and con's of building your own fsaverage? All the best, Silas I searched the mailing stream and found this answer: 'make_average_subject script, but as Doug implies you probably don't need to. Our warp is high-enough dimensional that you rarely need to build average subjects from your own population' ___ 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.
[Freesurfer] Structural analysis
Dear FreeSurfer team, Repost: Please let me know if the answers are too obvious or the questions are inappropriate for this forum! I'm currently doing a structural FS analysis with 50 Multiple Sclerosis (MS) patients and 25 Healthy Controls (HC). FLAIR-lesions were drawn onto the aseg.mgz as White Matter Hypointensities (=77). I've finished the analysis, but have some questions regarding my results. Results: HC (n=25) MS (n=50) p-value Mean TIV (SD) [ml] 1594.9 (154.7) 1559.5 (140.1) > 0.05 Mean WMV (SD) [ml] 503.6 (57.3) 485.2 (59.5) > 0.05 Mean GMV (SD) [ml] 657.2 (69.9) 635.1 (47.9) > 0.05 Mean WMHV (SD) [ml] 1.12 (0.4) 5.97 (5.7) 0.677 1) Does these results look trustworthy/reliable? WMV < GMV? 2) What is the difference between WMV+GMV and TIV? CSF? Ventricles? 3) I find no atrophy in the MS patients? Do you have an idea why? If not, don't answer this. 4) What is White Matter Hypointensities comprised of in HC? 5) What is the best estimate of total white matter volume? Best, Silas ___ 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. ___ 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.
[Freesurfer] Structural analysis
Dear FreeSurfer team, I'm currently doing a structural FS analysis with 50 Multiple Sclerosis (MS) patients and 25 Healthy Controls (HC). FLAIR-lesions were drawn onto the aseg.mgz as White Matter Hypointensities (=77). I've finished the analysis, but have some questions regarding my results. Results: HC (n=25) MS (n=50) p-value Mean TIV (SD) [ml] 1594.9 (154.7) 1559.5 (140.1) > 0.05 Mean WMV (SD) [ml] 503.6 (57.3) 485.2 (59.5) > 0.05 Mean GMV (SD) [ml] 657.2 (69.9) 635.1 (47.9) > 0.05 Mean WMHV (SD) [ml] 1.12 (0.4) 5.97 (5.7) 0.677 1) Does these results look correct? WMV < GMV? 2) What is the difference between WMV+GMV and TIV? CSF? Ventricles? 3) I find no atrophy in the MS patients; are there reported any problems with FS and MS patients? 4) What is White Matter Hypointensities comprised of in HC? Best, Silas ___ 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.
Re: [Freesurfer] I receive an error when running recon-all with T1 and lesions from FLAIR
Thanks again Douglas! Your time and help is greatly appreciated!
Best, Silas
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve
<gr...@nmr.mgh.harvard.edu>
Sent: Thursday, August 25, 2016 4:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] I receive an error when running recon-all with T1 and
lesions from FLAIR
MRIwrite() writes out the image as a float, whereas FS insists that it
be UCHAR or INT. To get this, run
mri_convert aseg.mgz -odt int --no_scale 1 aseg.mgz
View aseg.mgz to make sure it looks right, then rerun recon-all
-autorecon2-cp -autorecon3
On 08/24/2016 05:51 PM, Silas wrote:
>
> Dear FreeSurfer team,
>
>
> I'm doing a structural analysis with 50 MS patients and 50 healthy
> controls (T1, T2 and FLAIR). The MS patients have multiple lesions
> mainly in white matter. My co-worker did manual editing (bullet
> points) in the FLAIR images, and i would like to use these edits when
> running recon-all in order to avoid further manual editing.
>
>
> _Steps in analysis:_
>
>
> 1) First steps of recon-all:
>
> recon-all -autorecon1 -autorecon2
>
>
> 2) Reslicing the FLAIR images:
>
> The aseg.auto.mgz (256x256x256) didn't have the same size as the
> FLAIR (resliced to 1mm, co-registered in MNI-space and with manually
> drawn binary lesion masks (218x182x182)). I overcome this problem by
> reslicing the FLAIR images using aseg.auto.nii as the image defining
> space. This was done in SPM8, and prior to this the aseg.auto.mgz was
> converted to a .nii using mri_convert.
>
>
> 3) Insert lesions from the resliced FLAIR images to aseg.mgz:
>
> aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg
>
> manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever
> format, but should be binary
>
> ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol ~= 0);
>
> newaseg = aseg;
>
> newaseg.vol(ind) = 77;
>
> MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so
> make a backup
>
>
> 4) The last steps of recon-all:
>
> recon- all -autorecon2-cp -autorecon3
>
> When running the following command i get this error:
>
> /depot64/freesurfer/freesurfer.5.3.0/bin/recon-all -s 01MS
> -autorecon2-cp -autorecon3 subjid 01MS
>
>
>
>
> '#@# Intensity Normalization2 Mon Aug DATE
> /.../subjects_FLAIR/01MS/mri
>
> mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> using segmentation for initial intensity normalization
> using MR volume brainmask.mgz to mask input volume...
> reading from norm.mgz...
> Reading aseg aseg.mgz
> normalizing image...
> processing with aseg
> removing outliers in the aseg WM...
> 5361 control points removed
> Building bias image
> mriMarkUnmarkedNeighbors: all inputs must be MRI_UCHAR or MRI_INT
> building Voronoi diagram...
> Numerical argument out of domain
> Linux big28 3.13.0-66-generic #108-Ubuntu SMP Wed Oct 7 15:20:27 UTC
> 2015 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s 01MS exited with ERRORS at Mon Aug 8 15:31:32 CEST 2016
>
> *The lesions looks alright (as if they are in the right place). Do you
> have any suggestions what to do if they are not? And what could be the
> problem if they are placed correctly?*
>
> *What is the advantage of starting by running autorecon-1 and 2 and
> then inserting the lesions from the FLAIR?*
>
>
> Thanks a lot for all your help!
>
>
> Best, Silas
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
mail.nmr.mgh.harvard.edu
To see the collection of prior postings to the list, visit the Freesurfer
Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
--
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
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contains patient inf
[Freesurfer] I receive an error when running recon-all with T1 and lesions from FLAIR
Dear FreeSurfer team,
I'm doing a structural analysis with 50 MS patients and 50 healthy controls
(T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white
matter. My co-worker did manual editing (bullet points) in the FLAIR images,
and i would like to use these edits when running recon-all in order to avoid
further manual editing.
Steps in analysis:
1) First steps of recon-all:
recon-all -autorecon1 -autorecon2
2) Reslicing the FLAIR images:
The aseg.auto.mgz (256x256x256) didn't have the same size as the FLAIR
(resliced to 1mm, co-registered in MNI-space and with manually drawn binary
lesion masks (218x182x182)). I overcome this problem by reslicing the FLAIR
images using aseg.auto.nii as the image defining space. This was done in SPM8,
and prior to this the aseg.auto.mgz was converted to a .nii using mri_convert.
3) Insert lesions from the resliced FLAIR images to aseg.mgz:
aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg
manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever format, but
should be binary
ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol ~= 0);
newaseg = aseg;
newaseg.vol(ind) = 77;
MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so make a
backup
4) The last steps of recon-all:
recon- all -autorecon2-cp -autorecon3
When running the following command i get this error:
/depot64/freesurfer/freesurfer.5.3.0/bin/recon-all -s 01MS -autorecon2-cp
-autorecon3 subjid 01MS
'#@# Intensity Normalization2 Mon Aug DATE
/.../subjects_FLAIR/01MS/mri
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
Reading aseg aseg.mgz
normalizing image...
processing with aseg
removing outliers in the aseg WM...
5361 control points removed
Building bias image
mriMarkUnmarkedNeighbors: all inputs must be MRI_UCHAR or MRI_INT
building Voronoi diagram...
Numerical argument out of domain
Linux big28 3.13.0-66-generic #108-Ubuntu SMP Wed Oct 7 15:20:27 UTC 2015
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 01MS exited with ERRORS at Mon Aug 8 15:31:32 CEST 2016
The lesions looks alright (as if they are in the right place). Do you have any
suggestions what to do if they are not? And what could be the problem if they
are placed correctly?
What is the advantage of starting by running autorecon-1 and 2 and then
inserting the lesions from the FLAIR?
Thanks a lot for all your help!
Best, Silas
___
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.
[Freesurfer] Structural group analysis
Dear FreeSurfer team, I'm doing a structural analysis with around 20 subjects and I'm specifically interested in the areas premotor cortex and primary motor cortex. By matlab analysis I've found a very strong statistical significant difference in the cortical thickness when comparing these two areas with all subjects (data extracted from FreeSurfer recon-all pipeline). I would like to visualize these results on the surface of fsaverage, and I'm familiar with the FreeSurfer group analysis pipeline. So far I've simply made a OSGM group analysis and visualized these results on the fsaverage in a premade label of premotor cortex and primary motor cortex and correlated for multiple comparisons using your precomputed monte carlo simulation - but this doesn't make it. Do you guys have a clever way to visualize these results in FreeSurfer? I have one group and would like to visualize the difference between two areas. I've thought about presenting each subject two times in the FSGD-file (primary motor cortex and premotor cortex), but this isn't possible and seems as a clumsy way to solve this problem. Please let me know if my problem is incomprehensible! Best, Silas ___ 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.
Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR
Hi Douglas,
It seems that the lesions are in the right place. Do you have other suggestions?
I just want to make sure; when you wrote: ind = find( (aseg.vol == 2 | aseg.vol
== 41) & manlesion.vol != 0); -> you meant: ind = find( (aseg.vol == 2 |
aseg.vol == 41) & manlesion.vol ~= 0);
Best, Silas
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve
<gr...@nmr.mgh.harvard.edu>
Sent: Wednesday, August 10, 2016 11:56 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR
did you look at the aseg.mgz to see if the lesions were in the right place?
On 08/10/2016 03:28 AM, Silas wrote:
>
> Thank you very much for your help Douglas!
>
>
> I had a few problems running these commands.
>
> 1) recon-all -autorecon1 -autorecon2 -> no problems
>
>
> 2) The matlab script
>
> The aseg.auto.mgz (256x256x256) didn't have the same size as the FLAIR
> (resliced to 1mm, co-registered in MNI-space and with manually drawn
> binary lesion masks (218x182x182)). I overcome this problem by
> reslicing the FLAIR image and using aseg.auto.nii as the image
> defining space. This was done in SPM8, and prior to this the
> aseg.auto.mgz was converted to a .nii using mri_convert.
>
> This seemed to solve the problem!
>
>
> 3) recon- all -autorecon2-cp -autorecon3
>
> When running the following command i get this error:
>
> /depot64/freesurfer/freesurfer.5.3.0/bin/recon-all -s 01MS
> -autorecon2-cp -autorecon3 subjid 01MS
>
>
>
>
> '#@# Intensity Normalization2 Mon Aug DATE
> /.../subjects_FLAIR/01MS/mri
>
> mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> using segmentation for initial intensity normalization
> using MR volume brainmask.mgz to mask input volume...
> reading from norm.mgz...
> Reading aseg aseg.mgz
> normalizing image...
> processing with aseg
> removing outliers in the aseg WM...
> 5361 control points removed
> Building bias image
> mriMarkUnmarkedNeighbors: all inputs must be MRI_UCHAR or MRI_INT
> building Voronoi diagram...
> Numerical argument out of domain
> Linux big28 3.13.0-66-generic #108-Ubuntu SMP Wed Oct 7 15:20:27 UTC
> 2015 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s 01MS exited with ERRORS at Mon Aug 8 15:31:32 CEST 2016
>
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting'
BugReporting - Free Surfer
Wiki<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
surfer.nmr.mgh.harvard.edu
top. Bug Reporting. Submitting a request for help . When submitting a request
for help with your problems please be aware that the developers will try and
repeat your ...
>
> *How can i solve this problem?*
>
>
> Best, Silas
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
> <gr...@nmr.mgh.harvard.edu>
> *Sent:* Tuesday, August 2, 2016 4:06 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR
>
> That recon-all command will not work as the FLAIR input should be a
> simple FLAIR image. The FLAIR will only correct the pial surface and
> will have nothing to do with lesion segmentation. Emily Lindermer has
> a tool that can take a T1 and FLAIR and produce a lesion map; but
> given that you already have manual segmentations, maybe that is not so
> helpful. One thing you can do is to edit the aseg.mgz to insert your
> lesions. First run recon-all with -autorecon1 -autorecon2 instead of
> -all. Then, in matlab,
>
>
> aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg
>
> manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever
> format, but should be binary
>
> ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol != 0);
>
> newaseg = aseg;
>
> newaseg.vol(ind) = 77;
>
> MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so
> make a backup
>
>
> Then run recon-all with -autorecon2-cp -autorecon3
>
>
>
> On 8/1/16 7:35 AM, Silas wrote:
>>
>>
>> Dear FreeSurfer team,
>>
>>
>> I'm doing a structural analysis with 50 MS patients and 50 healthy
>> controls (T1, T2 and FLAIR). The MS patients have multiple lesions
>> mainly in white matter. My co-worker did manual editing (bullet
>> points) in the FLAIR images, and i would like to use these edits when
>> running recon-all in order to avoid further manual editing.
>>
>>
>> The data i'm working
Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR
Thank you very much for your help Douglas!
I had a few problems running these commands.
1) recon-all -autorecon1 -autorecon2 -> no problems
2) The matlab script
The aseg.auto.mgz (256x256x256) didn't have the same size as the FLAIR
(resliced to 1mm, co-registered in MNI-space and with manually drawn binary
lesion masks (218x182x182)). I overcome this problem by reslicing the FLAIR
image and using aseg.auto.nii as the image defining space. This was done in
SPM8, and prior to this the aseg.auto.mgz was converted to a .nii using
mri_convert.
This seemed to solve the problem!
3) recon- all -autorecon2-cp -autorecon3
When running the following command i get this error:
/depot64/freesurfer/freesurfer.5.3.0/bin/recon-all -s 01MS -autorecon2-cp
-autorecon3 subjid 01MS
'#@# Intensity Normalization2 Mon Aug DATE
/.../subjects_FLAIR/01MS/mri
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
Reading aseg aseg.mgz
normalizing image...
processing with aseg
removing outliers in the aseg WM...
5361 control points removed
Building bias image
mriMarkUnmarkedNeighbors: all inputs must be MRI_UCHAR or MRI_INT
building Voronoi diagram...
Numerical argument out of domain
Linux big28 3.13.0-66-generic #108-Ubuntu SMP Wed Oct 7 15:20:27 UTC 2015
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 01MS exited with ERRORS at Mon Aug 8 15:31:32 CEST 2016
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting'
How can i solve this problem?
Best, Silas
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
<gr...@nmr.mgh.harvard.edu>
Sent: Tuesday, August 2, 2016 4:06 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR
That recon-all command will not work as the FLAIR input should be a simple
FLAIR image. The FLAIR will only correct the pial surface and will have nothing
to do with lesion segmentation. Emily Lindermer has a tool that can take a T1
and FLAIR and produce a lesion map; but given that you already have manual
segmentations, maybe that is not so helpful. One thing you can do is to edit
the aseg.mgz to insert your lesions. First run recon-all with -autorecon1
-autorecon2 instead of -all. Then, in matlab,
aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg
manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever format, but
should be binary
ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol != 0);
newaseg = aseg;
newaseg.vol(ind) = 77;
MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so make a
backup
Then run recon-all with -autorecon2-cp -autorecon3
On 8/1/16 7:35 AM, Silas wrote:
Dear FreeSurfer team,
I'm doing a structural analysis with 50 MS patients and 50 healthy controls
(T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white
matter. My co-worker did manual editing (bullet points) in the FLAIR images,
and i would like to use these edits when running recon-all in order to avoid
further manual editing.
The data i'm working with is already resliced to 1 mm and co-registered in
MNI-space.
1) Can i use this data or would it be preferable to use the original T1's?
My thought was to run the following command:
recon-all -subject subjectname -i /path/to/input_volume -FLAIR
/path/to/FLAIR_volume_with_edits -FLAIRpial -all
2) Does this look correct? Is there anything i should be aware of? -> update:
Does this command only improve the pial surface? How can i also improve the
white mater segmentation (white) using FLAIR corrections?
3) Does it make a difference running recon-all -all with the FLAIR image -
compared to running recon-all -autorecon3 with the FLAIR after running
recon-all -all with only the T1?
4) I've also thought about using the lesion segmentation toolbox for SPM and
completely avoid manual editing - is this preferable to using the FLAIR with
manual editing?
5) How is the general strength of analysing corpus callosum structurally in MS
patients using FreeSurfer?
Best, Silas
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was s
[Freesurfer] Fw: Running recon-all with T1 and FLAIR
Dear FreeSurfer team, I'm doing a structural analysis with 50 MS patients and 50 healthy controls (T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white matter. My co-worker did manual editing (bullet points) in the FLAIR images, and i would like to use these edits when running recon-all in order to avoid further manual editing. The data i'm working with is already resliced to 1 mm and co-registered in MNI-space. 1) Can i use this data or would it be preferable to use the original T1's? My thought was to run the following command: recon-all -subject subjectname -i /path/to/input_volume -FLAIR /path/to/FLAIR_volume_with_edits -FLAIRpial -all 2) Does this look correct? Is there anything i should be aware of? -> update: Does this command only improve the pial surface? How can i also improve the white mater segmentation (white) using FLAIR corrections? 3) Does it make a difference running recon-all -all with the FLAIR image - compared to running recon-all -autorecon3 with the FLAIR after running recon-all -all with only the T1? 4) I've also thought about using the lesion segmentation toolbox for SPM and completely avoid manual editing - is this preferable to using the FLAIR with manual editing? 5) How is the general strength of analysing corpus callosum structurally in MS patients using FreeSurfer? Best, Silas ___ 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.
[Freesurfer] Running recon-all with T1 and FLAIR
Dear FreeSurfer team, I'm doing a structural analysis with 50 MS patients and 50 healthy controls (T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white matter. My co-worker did manual editing (bullet points) in the FLAIR images, and i would like to use these edits when running recon-all in order to avoid further manual editing. The data i'm working with is already resliced to 1 mm and co-registered in MNI-space. 1) Can i use this data or would it be preferable to use the original T1's? My thought was to run the following command: recon-all -subject subjectname -i /path/to/input_volume -FLAIR /path/to/FLAIR_volume_with_edits -FLAIRpial -all 2) Does this look correct? Is there anything i should be aware of? 3) Does it make a difference running recon-all -all with the FLAIR image - compared to running recon-all -autorecon3 with the FLAIR after running recon-all -all with only the T1? 4) I've also thought about using the lesion segmentation toolbox for SPM and completely avoid manual editing - is this preferable to using the FLAIR with manual editing? 5) How is the general strength of analysing corpus callosum structurally in MS patients using FreeSurfer? Best, Silas ___ 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.
Re: [Freesurfer] How to find the difference between to different fMRI datasets?
Thanks Douglas! 1 - I have two functional files per subject (.mgh). Is it possible to insert two files per subject in mris_preproc? In my former functional analysis I haven't concatenated my data using a FSGD-file when running mris_preproc. 2 - Can you calculate the difference between two functional data sets (on the fsaverage) before starting the group analysis stream? E.g. by subtracting the files? Best, Silas From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Thursday, March 3, 2016 6:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to find the difference between to different fMRI datasets? Create a contrast between the two conditions On 03/01/2016 01:27 AM, Silas wrote: > > Dear FreeSurfer team, > > > Thank you for all your help so far! > > > I would like to visualize the difference between two fMRI data sets. > > Data set1: Cortical activation during movement of a finger. > > Data set2: Cortical activation during movement of a finger different > from the first finger. > > > How can i perform this operation? > > > Best, Silas > > > > ___ > 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/ ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How to find the difference between to different fMRI datasets?
Dear FreeSurfer team, Thank you for all your help so far! I would like to visualize the difference between two fMRI data sets. Data set1: Cortical activation during movement of a finger. Data set2: Cortical activation during movement of a finger different from the first finger. How can i perform this operation? Best, Silas ___ 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.
Re: [Freesurfer] FreeSurfer group analysis: mri_glmfit-sim
Dear FS team, I followed the BuildYourOwnMonteCarlo guide and received an error running mri_glmfit-sim. This might be a simple problem but I have troubles finding the flaw. Hopefully you can help me out. Commands: % step 1: If not done already - create the label: mri_annotation2label --subject fsaverage --hemi rh --outdir labeldir % step 2: mri_mcsim using my own label on the fsaverage surface: mri_mcsim --o .../S1M1_GroupAnalysis/S1M1 --base mc-z --save-iter --surf fsaverage rh --nreps 1 --label .../S1M1_GroupAnalysis/S1M1.label % step 3: mri_glmfit investigating the correlation between an AUC value and t1t2ratio mri_glmfit --y rh.t1t2ratio_fmed_3sm_decurv.fsavg.5.mgh --fsgd AUC.fsgd --surf fsaverage rh --C intercept.mtx --C slope.mtx --label S1M1.label --o t1t2vsAUC_S1M1.5.glmdir % step 4: mris_glmfit-sim mri_glmfit-sim --glmdir t1t2vsAUC_S1M1.5.glmdir --cache-dir .../S1M1_GroupAnalysis/S1M1 --cache 2 pos --cwp 0.05 Error: ERROR: cannot find .../S1M1_GroupAnalysis/S1M1/fsaverage/rh/cortex/fwhm09/pos/th20/mc-z.csd Question: Is there any obvious flaws in my commands? In the guide I'm suggested to place my results into $FREESURFER_HOME/... is this a necessity? How does mri_glmfit-sim recognizes that I'm investigating the label S1M1 and not cortex? Could i simply just copy-paste my results from mri_mcsim into .../S1M1_GroupAnalysis/S1M1/fsaverage/rh/cortex/ ? Best, Silas From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <gr...@nmr.mgh.harvard.edu> Sent: Monday, February 8, 2016 4:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer group analysis: mri_glmfit-sim On 2/7/16 1:34 PM, Silas wrote: Dear FS team, I'm currently making a group analysis using the "command-line" group analysis stream in freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng [https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> FsTutorial/GroupAnalysisDng - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> surfer.nmr.mgh.harvard.edu Introduction. This tutorial is designed to introduce you to the "command-line" group analysis stream in FreeSurfer (as opposed to QDEC which is GUI-driven), including ... 1) I would like to do a surface based analysis where i'm only investigating a certain area or label - instead of doing a whole brain analysis. This can be done by introducing --label surface_area_of_interest.label when running mri_glmfit. Would this (in theory) give me different results from doing a whole brain analysis - or would it just exclude the results from outside the label? No. However, if your activation is near the boundary of the ROI, then you may want to constrain the spatial smoothing to be within the ROI. And how about after clusterwise correction for multiple comparisons? If your new ROI is much smaller than whole hemisphere, then you will need to generate new correction tables (otherwise it won't help to constrain it to an ROI). To do this, see https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo -> is there a better way to do this than following the command-line group analysis stream in freesurfer? No 2) When running mri_glmfit-sim i'm investigating the output ending with -voxel.mgh - how do i interpret the results of this file? When investigating the file in freeview what is the meaning of the units when configuring the overlay? This is the voxel-wise correction for multiple comparisons. The value of the voxel (and overlay config units) are -log10(p), where p is the p-value corrected for multiple comparisons. So p=.01 means 2. Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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.
[Freesurfer] FreeSurfer group analysis: mri_glmfit-sim
Dear FS team, I'm currently making a group analysis using the "command-line" group analysis stream in freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng [https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> FsTutorial/GroupAnalysisDng - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> surfer.nmr.mgh.harvard.edu Introduction. This tutorial is designed to introduce you to the "command-line" group analysis stream in FreeSurfer (as opposed to QDEC which is GUI-driven), including ... 1) I would like to do a surface based analysis where i'm only investigating a certain area or label - instead of doing a whole brain analysis. This can be done by introducing --label surface_area_of_interest.label when running mri_glmfit. Would this (in theory) give me different results from doing a whole brain analysis - or would it just exclude the results from outside the label? And how about after clusterwise correction for multiple comparisons? -> is there a better way to do this than following the command-line group analysis stream in freesurfer? 2) When running mri_glmfit-sim i'm investigating the output ending with -voxel.mgh - how do i interpret the results of this file? When investigating the file in freeview what is the meaning of the units when configuring the overlay? Best, Silas ___ 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.
[Freesurfer] Fw: FreeSurfer group analysis: mri_glmfit-sim
Dear FS team, I'm currently making a group analysis using the "command-line" group analysis stream in freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng [https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> FsTutorial/GroupAnalysisDng - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> surfer.nmr.mgh.harvard.edu Introduction. This tutorial is designed to introduce you to the "command-line" group analysis stream in FreeSurfer (as opposed to QDEC which is GUI-driven), including ... 1) I would like to do a surface based analysis where i'm only investigating a certain area or label - instead of doing a whole brain analysis. This can be done by introducing --label surface_area_of_interest.label when running mri_glmfit. Would this (in theory) give me different results from doing a whole brain analysis - or would it just exclude the results from outside the label? And how about after clusterwise correction for multiple comparisons? -> is there a better way to do this than following the command-line group analysis stream in freesurfer? 2) When running mri_glmfit-sim i'm investigating the output ending with -voxel.mgh - how do i interpret the results of this file? When investigating the file in freeview what is the meaning of the units when configuring the overlay? Best, Silas ___ 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.
[Freesurfer] FreeSurfer group analysis: mri_glmfit-sim
Dear FS team, I'm currently making a group analysis using the "command-line" group analysis stream in freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng [https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> FsTutorial/GroupAnalysisDng - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> surfer.nmr.mgh.harvard.edu Introduction. This tutorial is designed to introduce you to the "command-line" group analysis stream in FreeSurfer (as opposed to QDEC which is GUI-driven), including ... 1) I would like to do a surface based analysis where i'm only investigating a certain area or label - instead of doing a whole brain analysis. This can be done by introducing --label surface_area_of_interest.label when running mri_glmfit. Would this give me different results from doing a whole brain analysis - or would it just exclude the results from outside the label? And how about after clusterwise correction for multiple comparisons? -> is there a better way to do this than following the command-line group analysis stream in freesurfer? 2) When running mri_glmfit-sim i'm investigating the output ending with -voxel.mgh - how do i interpret the results of this file? When investigating the file in freeview what is the meaning of the units when configuring the overlay? Best, Silas ___ 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.
[Freesurfer] Multimodality analysis in FreeSurfer
Dear Freesurfer team, I've scanned a group of subjects and gained structural and myelination data. Then, I've used mris_preproc to map the data onto the surface of fsaverage (and concatenating the data). I would like to investigate the correlation between cortical thickness and myelination by mapping this correlation onto the fsaverage (an one sample group mean analysis) - is this possible? Do you have an existing guide approaching this problem? Thank you! Best, Silas ___ 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.
Re: [Freesurfer] Multimodality analysis in FreeSurfer
I've mapped cortical thickness and the myelination data onto the fsaverage, and also used general linear modelling to investigate the one sample group mean of myelination data og cortical thickness (not very useful since the mean thickness or myelination should never be 0) data separately. I would like to map the correlation between cortical thickness and myelination onto the fsaverage. I've investigated this statistical correlation by a vertex wise correlation study in matlab, and it should be possible to map this onto the fsaverage. Though, I would like to perform this correlation study entirely in FreeSurfer - in this way I would easily be able to correlate for multiple comparisons using the standardized pipeline for FreeSurfer group analysis. Best, Silas From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Tuesday, November 17, 2015 7:10 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Multimodality analysis in FreeSurfer I'm not sure what you mean. You say that you have mapped the thickness and myelin data into fsaverage space but then need to map the correlation into fsaverage. Isn't it already there? On 11/17/2015 10:33 AM, Silas wrote: > > Dear Freesurfer team, > > > I've scanned a group of subjects and gained structural and myelination > data. Then, I've used mris_preproc to map the data onto the surface of > fsaverage (and concatenating the data). I would like to investigate > the correlation between cortical thickness and myelination by mapping > this correlation onto the fsaverage (an one sample group mean > analysis) - is this possible? Do you have an existing guide > approaching this problem? > > > Thank you! > > > Best, Silas > > > > ___ > 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/ ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Smoothing of functional data mapped onto the fsaverage surface
Dear Freesurfer, 1) I would like to investigate the possible outcomes of my functional group analysis after smoothing with 5 FWHM and 10 FWHM. My functional data is already mapped onto the fsaverage. Which command would you suggest for smoothing this data? 2) In the functional group analysis tutorial there is a input to mri_glmfit called --wls cesvar.nii.gz which is the variance of each session at each voxel. How do i get this file? And what is the importance of doing this de-weighting of sessions with a high variance? Thanks! Best, Silas ___ 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.
[Freesurfer] mris_preproc -iv option
Dear Freesurfer team, How does mris_preproc map volume data onto the surface when using the -iv option? Is an average between the white and pial boundaries taken, or are only the voxels taken into account that intersect with one of the two surfaces (and if yes, with which surface)? mris_preproc--iv volmeasfileSpecify full path to a volume file and its registration matrix file. The registration matrix file is of the type accepted/created by tkregister2. The volume is sampled to the surface, and the result is used as the input surface measure. This is an alternative to using --meas. This still requires that a subject list be supplied. Thanks again! Best, Silas ___ 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.
[Freesurfer] Creating proper FSGD file
Hi Freesurfer team, I'm currently working on a functional group analysis using GLM (i've mapped my data onto the fsaverage). My problem is that I have more than one functional *.mgh file per subject, and i have troubles creating a proper FSGD file where i'm presenting each subject several times (btw i'm using mri_glmfit). 1) The solution to this problem might be to average (or sum) the *.mgh files of each subject and implement this average file in the FSGD. Which command is able to do this?2) Another solution to this problem is to present the subjects several times in the FSGD file or presenting several functional *.mgh files per subject in the FSGD file. Is this possible? I've tried to use mris_preproc to concatenate the files and presenting the output files in mri_glmfit - but this does not seem to be the solution since mris_preproc only concatenates the files. Thank you for your help, Best, Silas ___ 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.
Re: [Freesurfer] How to deal with labels and structural data
Hi Bruce, I would like to make a ROI analysis where i'll investigate cortical thickness of the labels - and afterwards use the labels to make a ROI analysis of fMRI data and t1t2ratio data which is mapped onto the fsaverage (I've already made an analysis on the surface). My question is how to investigate e.g. cortical thickness of the labels. What command do i use? Do i have to run recon-all again with the new label (and if, which steps of recon-all is necessary to re-run?)? Thanks! Best, Silas Date: Tue, 21 Jul 2015 10:53:02 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to deal with labels and structural data Hi Silas what do you want to do with the labels? As for whether to do it on fsaverage or individuals, you could start with fsaverage and map it to your other subjects and see how accurate it looks cheers Bruce On Tue, 21 Jul 2015, Silas wrote: Dear Freesurfer team, I've created my own labels using tksurfer and common anatomical guidelines - and my next step is to apply these labels to my subjects and analyze (ROI) cortical thickness or volume (first of all), functional data and myelination data. 1 - Do you suggest drawing a label on the surface of fsaverage and applying this label to the other subjects (e.g. using mri_label2label) - or drawing a label on each subjects surface? 2 - What is my next step? Do i have to run recon-all again with my new label in the labels folder - or should i experiment with mri_label2vol and mri_label2annot? 3 - Do you have an existing guide in this kind of analysis? Thanks! Best, Silas ___ 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. ___ 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.
[Freesurfer] How to deal with labels and structural data
Dear Freesurfer team, I've created my own labels using tksurfer and common anatomical guidelines - and my next step is to apply these labels to my subjects and analyze (ROI) cortical thickness or volume (first of all), functional data and myelination data.1 - Do you suggest drawing a label on the surface of fsaverage and applying this label to the other subjects (e.g. using mri_label2label) - or drawing a label on each subjects surface?2 - What is my next step? Do i have to run recon-all again with my new label in the labels folder - or should i experiment with mri_label2vol and mri_label2annot?3 - Do you have an existing guide in this kind of analysis? Thanks! Best, Silas ___ 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.
Re: [Freesurfer] FW: FW: Functional group analysis
Hi Bruce, I will. Thanks! Best, Silas Date: Sun, 28 Jun 2015 13:20:30 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: FW: Functional group analysis Hi Silas Doug (who normally answers this kind of question) is on vacation. Can you repost in a few days? cheers Bruce On Sun, 28 Jun 2015, Silas wrote: Dear all, Can anyone help me with this question? Best, Silas From: silasniel...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Wed, 24 Jun 2015 11:35:28 +0200 Subject: [Freesurfer] FW: Functional group analysis Dear FreeSurfer team, I'm working on a functional analysis using FreeSurfer. I've already preprocessed my fMRI data and now I would like to analyze this data using mri_glmfit. My input is the prepared beta estimates for the fmri data (regression coefficients) and two groups (with activated regions for different muscles in the hand; musculus abductor digiti minimi vs first dorsal interossei). I do not want to smooth my data. Which command/step do you suggest in order to implement this data into mri_glm? I've experimented with mris_preproc and the creation of a FSGD-file in the structural analysis in order to implement my data in the GLM. Best, Silas From: silasniel...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Functional group analysis Date: Fri, 19 Jun 2015 14:26:20 +0200 Dear FreeSurfer team, I'm currently doing a functional group analysis using FreeSurfer by following yourtutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFa stGroupLevel - in order to concatenate the subjects data into one file you suggest using the command isxconcat-sess. My questions is; is it possible to use the command mris_preproc as in the structural analysis in this step? I simply want to project functional beta-values onto the fsaverage surface and analyze if there is a statistical significant difference between two groups (after correcting for multiple comparisons). Best, Silas ___ 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. ___ 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.___ 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.
[Freesurfer] FW: FW: Functional group analysis
Dear all, Can anyone help me with this question? Best, Silas From: silasniel...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Wed, 24 Jun 2015 11:35:28 +0200 Subject: [Freesurfer] FW: Functional group analysis Dear FreeSurfer team, I'm working on a functional analysis using FreeSurfer. I've already preprocessed my fMRI data and now I would like to analyze this data using mri_glmfit. My input is the prepared beta estimates for the fmri data (regression coefficients) and two groups (with activated regions for different muscles in the hand; musculus abductor digiti minimi vs first dorsal interossei). I do not want to smooth my data. Which command/step do you suggest in order to implement this data into mri_glm? I've experimented with mris_preproc and the creation of a FSGD-file in the structural analysis in order to implement my data in the GLM. Best, Silas From: silasniel...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Functional group analysis Date: Fri, 19 Jun 2015 14:26:20 +0200 Dear FreeSurfer team, I'm currently doing a functional group analysis using FreeSurfer by following your tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel - in order to concatenate the subjects data into one file you suggest using the command isxconcat-sess. My questions is; is it possible to use the command mris_preproc as in the structural analysis in this step? I simply want to project functional beta-values onto the fsaverage surface and analyze if there is a statistical significant difference between two groups (after correcting for multiple comparisons). Best, Silas ___ 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.___ 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.
[Freesurfer] FW: Functional group analysis
Dear FreeSurfer team, I'm working on a functional analysis using FreeSurfer. I've already preprocessed my fMRI data and now I would like to analyze this data using mri_glmfit. My input is the prepared beta estimates for the fmri data (regression coefficients) and two groups (with activated regions for different muscles in the hand; musculus abductor digiti minimi vs first dorsal interossei). I do not want to smooth my data. Which command/step do you suggest in order to implement this data into mri_glm? I've experimented with mris_preproc and the creation of a FSGD-file in the structural analysis in order to implement my data in the GLM. Best, Silas From: silasniel...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Functional group analysis Date: Fri, 19 Jun 2015 14:26:20 +0200 Dear FreeSurfer team, I'm currently doing a functional group analysis using FreeSurfer by following your tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel - in order to concatenate the subjects data into one file you suggest using the command isxconcat-sess. My questions is; is it possible to use the command mris_preproc as in the structural analysis in this step? I simply want to project functional beta-values onto the fsaverage surface and analyze if there is a statistical significant difference between two groups (after correcting for multiple comparisons). Best, Silas ___ 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.
[Freesurfer] Functional group analysis
Dear FreeSurfer team, I'm currently doing a functional group analysis using FreeSurfer by following your tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel - in order to concatenate the subjects data into one file you suggest using the command isxconcat-sess. My questions is; is it possible to use the command mris_preproc as in the structural analysis in this step? I simply want to project functional beta-values onto the fsaverage surface and analyze if there is a statistical significant difference between two groups (after correcting for multiple comparisons). Best, Silas ___ 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.
[Freesurfer] Fsaverage template, labeling and group analysis
Dear Freesurfer team, I would like to create a label using the fsaverage template (tksurfer) and then map this label to my subjects. The problem is that i currently have several fsaverage folders; one in each subject folder. How do i get one single fsaverage file? And is it possible to create a label and afterwards map this label accurately to the rest of my subjects? Would you recommend to correct this label after mapping it to the subjects (for each individual subject)? Best, Silas ___ 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.
[Freesurfer] Average subject
Dear Freesurfer team, I now see that the fsaverage folder in each subject folder is just a shortcut to the freesurfer folder: 'freesurfer/freesurfer.5.3.0/subjects/fsaverage'. I have more questions regarding the fsaverage and creating a new label. Is it correctly understood that fsaverage is an average of all my subjects (that i create using the command -qcache when running recon-all)? Is the fsaverage file updated when making manual corrections to the pial and white matter surface when running recon-all without the -qcache function? Another thought is: Is it possible to create a average subject using make_average_subject - create a label in tksurfer using this average subject (i'm investigating dorsal premotor cortex and the handknob area) - and implement this label to all my subjects using mri_label2label - and at last correct this label manually in each subject individually (if needed)? Is this the correct way to approach my issue? Or would you rather recommend me to change an existing label? Group analysis guide: 'When you have run recon-all with the -qcache option, recon-all will resample data onto the average subject (fsaverage)' Bruce Fischl: 'sure, there are tools for drawing ROIs/labels on the surface in tksurfer. You can create a label on fsaverage or an individual subject, then use mri_label2label to map it to other subjects if you like'A last question is; after I've made my label and implemented it to all my subjects i would like to investigate cortical thickness of this particular part of the brain by a group analysis using freesurfer tools. Do you have an thorough guide to the steps in this analysis (in addition to this guide http://freesurfer.net/fswiki/FsTutorial/GroupAnalysis)? Thank you for all your help, Best, Silas ___ 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.
[Freesurfer] Labeling of handknob area in primary motor cortex
Dear freesurfer, I was also wondering if you have an existing label of the handknob area located in primary motor cortex? Best, Silas ___ 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.
[Freesurfer] Labeling of the dorsal part of BA6 (dorsal premotor cortex)
Dear freesurfer, Do you have an existing label of the dorsal part of the premotor cortex? If not, is it possible to manually label this area? Best, Silas ___ 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.
[Freesurfer] Changing wstresh and removing wsg-atlas - consequences?
Hi Freesurfer team, I'm currently making an structural analysis using freesurfer. In the analysis i'm comparing 3 groups; 2 patient groups with different reactions to a certain type of medication and a healthy control group. In the freesurfer pipeline i'm changing the parameters wsthresh and wsgatlas in order to obtain a better fitted pial surface and white matter surface - and i was wondering if changing these parameters affect the comparability of the 3 groups (if e.g. i would like to investigate the inferior frontal gyrus)? Best, Silas ___ 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.
Re: [Freesurfer] Changing wstresh and removing wsg-atlas - consequences?
Hi Bruce, Thanks for your answer. My data quality isn't always as good as i could have hoped. This unfortunately impairs freesurfers ability to distinguish between grey matter surface, dura and skull. In specific cases I've found it rewarding to change the parameters in order to gain a better fitting of the pial surface to the actual grey matter surface. Afterwards I've made manual editing to obtain the best possible fit. These parameter changes isn't group specific. Would you still avoid changing the parameters? Best, Silas Date: Mon, 16 Feb 2015 09:28:05 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Changing wstresh and removing wsg-atlas - consequences? Hi Silas you should certainly try to avoid a group-by-processing parameters bias. Is there a reason that one group would require different parameters than another? cheers Bruce On Mon, 16 Feb 2015, Silas wrote: Hi Freesurfer team, I'm currently making an structural analysis using freesurfer. In the analysis i'm comparing 3 groups; 2 patient groups with different reactions to a certain type of medication and a healthy control group. In the freesurfer pipeline i'm changing the parameters wsthresh and wsgatlas in order to obtain a better fitted pial surface and white matter surface - and i was wondering if changing these parameters affect the comparability of the 3 groups (if e.g. i would like to investigate the inferior frontal gyrus)? Best, Silas ___ 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. ___ 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.
Re: [Freesurfer] Changing wstresh and removing wsg-atlas - consequences?
Hi Christian, Thanks! My data quality is generally not very good - this i why i'm changing the parameters before starting manual editing (this saves me a lot of work). I just wanted to make sure that it did not affect the atlas more than necessary - making the data incomparable. Lets have a talk at DRCMR - i also have some questions concerning movement artefacts. Best, Silas Date: Mon, 16 Feb 2015 15:28:46 +0100 From: ct...@dtu.dk To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Changing wstresh and removing wsg-atlas - consequences? Hi Silas, Changing the wsthresh and wsgatlas parameters only affect the brainmask (which is, among other things, used to limit how far the pial surface is allowed to grow). This shouldn't affect the white matter. if your data contrast is good, you generally wont see much affect from adjusting these parameters. However, if the contrast is bad you need to inspect your brainmasks carefully, to make sure they improved (without removing actual brain from the image). Furthermore, in this case it is likely you'll also need to edit the brainmasks manually. To answer your question: Whenever you modify the parameters, and in particular if you need to edit brainmasks, you introduce a bias in your study (your qualitative evaluation of how good the brainmasks / pial surfaces are). You need to consider if adjusting brainmasks is better than letting the pipeline do its job - which boils down to the number of subjects you have. The more you have, the more robust your statistics will be, and the more likely it is that you can leave everything as it is. However, If you have few subjects, bad data quality (and in turn, brainmask quality) can really impact your pial surface, and then it may be best to adjust the masks. We can talk more at the hospital if you need further discussion, and also look at your data ;-) Best, Christian On 02/16/2015 01:54 PM, Silas wrote: Hi Freesurfer team, I'm currently making an structural analysis using freesurfer. In the analysis i'm comparing 3 groups; 2 patient groups with different reactions to a certain type of medication and a healthy control group. In the freesurfer pipeline i'm changing the parameters wsthresh and wsgatlas in order to obtain a better fitted pial surface and white matter surface - and i was wondering if changing these parameters affect the comparability of the 3 groups (if e.g. i would like to investigate the inferior frontal gyrus)? Best, Silas ___ 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. ___ 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.___ 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.
[Freesurfer] Labeling of preSMA?
Hi Freesurfer team, I'm currently investigating the volume of preSMA. Is there an existing label of preSMA? If not, together preSMA and SMA is also known as Brodmann Area 6, which is labeled already. PreSMA is located just rostrally to SMA in BA6, and i was wondering if it is possible to distinguish between preSMA and SMA by making a limit in y=0? Thanks, Best, Silas ___ 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.
[Freesurfer] Brodmann Area stats to table
Hi guys! Is there an easy way to get Brodmann Area stats to table like there is for aseg and aparc stats? Thanks! Silas PS. I looked the question up and it was answered in 2011 - I was just wondering if you guys made an easy way around the problem since then :) ___ 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.
[Freesurfer] Structural analysis
Hi all, I'm currently making a structural analysis on about 60 Parkinson patients and controls, and i would like to investigate specific regions in the brain - which do not seem to be included in the asegstats2table. How do i proceed from here? Best, Silas ___ 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.
Re: [Freesurfer] Freesurfer ROI analysis
Hi Bruce, Thanks for your help! But - would you recommend a longitudinal analysis even though i have quite many movement artefacts and bad scans - instead of just avoid using the worst picture? At the moment I'm making a cross-sectional study. I would also like to make an investigation of OFC grey matter thickness in the two groups; on and off medication (using freesurfer). Is Martin Reuther on vacation at the moment? Best, Silas Date: Fri, 25 Jul 2014 09:45:16 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer ROI analysis Hi Silas I'll leave the movement question for Martin Reuter who has been investigating this extensively. For your other question, one of the central focuses of our recent research has been in improving the sensitivity and reliability of longiudinal analyses like these, so it is definitely a major strength of ours. cheers Bruce On Fri, 25 Jul 2014, Silas wrote: Hi Freesurfer, I'm currently making a structural analysis on about 60 Parkinson's Disease patients using freesurfer - and i would like to make a ROI analysis. I have two MR pictures of each subject; a picture where the patients are on medication and an off medication picture (the medication is levodopa: Precursor to catecholamines e.g. dopamin). I would like to investigate the morphological differences in specific areas of the brain such as Nucleus Accumbens bilat., Orbitofrontal cortex bilat. and Anterior Cingulate Cortex. How would you consider freesurfer's strength in investigating differences in such specific areas in the brain? I have another question regarding movement artefacts. In a structural analysis would you remove pictures with movement artefacts if the segmentation after manual editing seems alright? Best, Silas ___ 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.___ 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.
[Freesurfer] Freesurfer ROI analysis
Hi Freesurfer, I'm currently making a structural analysis on about 60 Parkinson's Disease patients using freesurfer - and i would like to make a ROI analysis. I have two MR pictures of each subject; a picture where the patients are on medication and an off medication picture (the medication is levodopa: Precursor to catecholamines e.g. dopamin). I would like to investigate the morphological differences in specific areas of the brain such as Nucleus Accumbens bilat., Orbitofrontal cortex bilat. and Anterior Cingulate Cortex. How would you consider freesurfer's strength in investigating differences in such specific areas in the brain? I have another question regarding movement artefacts. In a structural analysis would you remove pictures with movement artefacts if the segmentation after manual editing seems alright? Best,Silas___ 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.
