Hi all,
I have a bunch of thickness files in fsaverage space (already smoothed at fwhm). I was wondering whether is possible to compute quickly an asymmetry overlay for each one, but it's turning more difficult than I thought. Vertex indices are different between lh and rh. So I started looking at fsaverage_sym, which has already registrations lh-rh. I thought this would be a nice shortcut to avoid registering every subject again. But there are a couple of confusing points:
1. Why isn't lh.inflated well aligned between fsaverage and fsaverage_sym (see figure below) ? [image: Inline image 1]
2. I found an old post in 2012 https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-December/026957.html, in which Donald advises to not run analyses on a simple left-right registration because one hemisphere would be more processed than the other. Since I might want to run some analyses, can you please explain what is the best way to get asymmetry surfaces (possibly by avoiding new registrations)? Why wouldn't a simple L-R registration of fsaverage be ok?
I run the analyses in R and don't necessarily need the glm tools within FS.
Thank you in advance. Dorian
A simple LR registration on fsaverage is not ok because you would be resampling one hemisphere and not another. The resampling inevitably incurs some interpolation so one hemi would be smoothed more than the other which would cause bias. If you just want something quick, then you can sample your fsaverage surfaces to fsaverage_sym (the registration has already been done in v6), then just follow the steps in the wiki using fsaverage as your subject name. I have not tested whether this is the same as doing the full xhemi process, so I would not use the results in publication. But probably they won't change much.
On 3/20/17 2:36 PM, Dorian P. wrote:
Hi all,
I have a bunch of thickness files in fsaverage space (already smoothed at fwhm). I was wondering whether is possible to compute quickly an asymmetry overlay for each one, but it's turning more difficult than I thought. Vertex indices are different between lh and rh. So I started looking at fsaverage_sym, which has already registrations lh-rh. I thought this would be a nice shortcut to avoid registering every subject again. But there are a couple of confusing points:
- Why isn't lh.inflated well aligned between fsaverage and
fsaverage_sym (see figure below) ? Inline image 1
- I found an old post in 2012
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-December/026957.html, in which Donald advises to not run analyses on a simple left-right registration because one hemisphere would be more processed than the other. Since I might want to run some analyses, can you please explain what is the best way to get asymmetry surfaces (possibly by avoiding new registrations)? Why wouldn't a simple L-R registration of fsaverage be ok?
I run the analyses in R and don't necessarily need the glm tools within FS.
Thank you in advance. Dorian
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Douglas.
I understand the rigor needed in the analysis and I agree. One more question for my curiosity.
My thickness maps are smoothed at 10mm before transferring in fsaverage space (mri_surf2surf --fwhm-src). After all this smoothing, does it still matter the subtle effects of interpolation on one hemisphere and not the other?
Dorian
On Wed, Mar 22, 2017 at 1:32 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
A simple LR registration on fsaverage is not ok because you would be resampling one hemisphere and not another. The resampling inevitably incurs some interpolation so one hemi would be smoothed more than the other which would cause bias. If you just want something quick, then you can sample your fsaverage surfaces to fsaverage_sym (the registration has already been done in v6), then just follow the steps in the wiki using fsaverage as your subject name. I have not tested whether this is the same as doing the full xhemi process, so I would not use the results in publication. But probably they won't change much.
On 3/20/17 2:36 PM, Dorian P. wrote:
Hi all,
I have a bunch of thickness files in fsaverage space (already smoothed at fwhm). I was wondering whether is possible to compute quickly an asymmetry overlay for each one, but it's turning more difficult than I thought. Vertex indices are different between lh and rh. So I started looking at fsaverage_sym, which has already registrations lh-rh. I thought this would be a nice shortcut to avoid registering every subject again. But there are a couple of confusing points:
- Why isn't lh.inflated well aligned between fsaverage and fsaverage_sym
(see figure below) ? [image: Inline image 1]
- I found an old post in 2012
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-December/026957.html, in which Donald advises to not run analyses on a simple left-right registration because one hemisphere would be more processed than the other. Since I might want to run some analyses, can you please explain what is the best way to get asymmetry surfaces (possibly by avoiding new registrations)? Why wouldn't a simple L-R registration of fsaverage be ok?
I run the analyses in R and don't necessarily need the glm tools within FS.
Thank you in advance. Dorian
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Yes, I think so. One hemi will be systematically different than the other, and this can easily be picked up in the stats
On 03/23/2017 10:07 AM, Dorian P. wrote:
Thank you Douglas.
I understand the rigor needed in the analysis and I agree. One more question for my curiosity.
My thickness maps are smoothed at 10mm before transferring in fsaverage space (mri_surf2surf --fwhm-src). After all this smoothing, does it still matter the subtle effects of interpolation on one hemisphere and not the other?
Dorian
On Wed, Mar 22, 2017 at 1:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
A simple LR registration on fsaverage is not ok because you would be resampling one hemisphere and not another. The resampling inevitably incurs some interpolation so one hemi would be smoothed more than the other which would cause bias. If you just want something quick, then you can sample your fsaverage surfaces to fsaverage_sym (the registration has already been done in v6), then just follow the steps in the wiki using fsaverage as your subject name. I have not tested whether this is the same as doing the full xhemi process, so I would not use the results in publication. But probably they won't change much. On 3/20/17 2:36 PM, Dorian P. wrote:Hi all, I have a bunch of thickness files in fsaverage space (already smoothed at fwhm). I was wondering whether is possible to compute quickly an asymmetry overlay for each one, but it's turning more difficult than I thought. Vertex indices are different between lh and rh. So I started looking at fsaverage_sym, which has already registrations lh-rh. I thought this would be a nice shortcut to avoid registering every subject again. But there are a couple of confusing points: 1. Why isn't lh.inflated well aligned between fsaverage and fsaverage_sym (see figure below) ? Inline image 1 2. I found an old post in 2012 <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-December/026957.html>, in which Donald advises to not run analyses on a simple left-right registration because one hemisphere would be more processed than the other. Since I might want to run some analyses, can you please explain what is the best way to get asymmetry surfaces (possibly by avoiding new registrations)? Why wouldn't a simple L-R registration of fsaverage be ok? I run the analyses in R and don't necessarily need the glm tools within FS. Thank you in advance. Dorian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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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