External Email - Use Caution
Thank you once more for your response, Bruce!
I intend to only use the parcellations that were initially mapped onto fsaverage and subsequently resampled to the subjects' native surfaces. This should ensure that the parcellations for all subjects are generated in the same way, right?
Many thanks again!
Best, Leo
Em dom., 10 de set. de 2023 às 15:55, Fischl, Bruce R.,PHD < BFISCHL@mgh.harvard.edu> escreveu:
External Email - Use CautionYes, 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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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
External Email - Use Caution *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 < BFISCHL@mgh.harvard.edu> escreveu:
External Email - Use Caution *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.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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