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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
<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
Subject: Re: [Freesurfer] Discrepancy in vertex counts between resampled and
recon-all generated annot files
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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:
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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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