10 Sep
2023
10 Sep
'23
1:34 p.m.
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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.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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