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Yes, although I expect the individual subject parcellations to be a bit more
accurate than the ones mapped from fsaverage. Probably not enough to make a
significant difference though
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Leonardo Cardoso Saraiva
Sent: Sunday, September 10, 2023 3:53 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Discrepancy in vertex counts between resampled and
recon-all generated annot files
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Many thanks for reaching out and providing such clear information, Douglas and
Bruce! I really appreciate it.
I was indeed comparing the ?h.aparc.annot files produced by recon-all to those
produced by mri_surf2surf.
The aim of my analyses is to compare groups in morphometric features, using
parcellations initially generated in fsaverage and then resampled to each
subject's native surface. Based on the information you provided, it sounds like
my approach is valid as long as I consistently use the mri_surf2surf command
with identical arguments for all subjects within each group. Is that correct?
Thanks again for your time and attention!
Best,
Leo
Em dom., 10 de set. de 2023 às 14:19, Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> escreveu:
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Actually there is a whole Bayesian segmentation on the surface procedure that
generates the individual subject parcellation so it definitely won’t be the
same as just mapping fsaverage
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Douglas N. Greve
Sent: Sunday, September 10, 2023 1:35 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Discrepancy in vertex counts between resampled and
recon-all generated annot files
External Email - Use Caution
Which annot files are you comparing? Some of them (eg, aparc) have an extra
procedure where the labels boundaries are fine-tuned, so that could cause the
difference. Your command looks right.
On 8/30/2023 1:28 PM, Leonardo Cardoso Saraiva wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I would like to follow up on my last email and ask if you had a chance to take
a look at it.
Any guidance or feedback would be greatly appreciated!
Thank you for your time!
Best,
Leo
Em dom., 20 de ago. de 2023 às 23:41, Leonardo Cardoso Saraiva
<leonardo.sara...@usp.br<mailto:leonardo.sara...@usp.br>> escreveu:
Dear Freesurfer Experts,
I am using .annot files to extract parcellated vertex-wise morphometric
features from surf files (e.g., area value from ?h.area file). For each vertex,
I want to determine the parcel it belongs to and its associated morphometric
features. During this process, I exclude vertices labeled as ‘unknown’ or
‘medial wall’.
In addition to the aparc parcellation, I am also using other parcellations
computed on fsaverage. Therefore, I need to resample these parcellations onto
native surfaces. To do this, I am using commands such as the one below:
mri_surf2surf --srcsubject fsaverage \
--sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\
--trgsubject sub-test \
--trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \
--hemi lh
As a sanity check, I used the above command to resample the aparc parcellation
onto native surfaces (which is already done by recon-all). However, when I use
the .annot files generated by the above command to extract morphometric
features from surf files, I get a different number of vertices than when I use
the .annot files generated by recon-all. Is this behavior expected? Am I doing
something wrong?
Thank you for your time and attention.
Best,
Leo
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