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

 



_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

 

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.