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

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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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

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.saraiva@usp.brmailto:leonardo.saraiva@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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