Cortical parcellation from Nifti volume - Various questions

Hi,

I’m a computer science student and I do my internship in a medical imaging laboratory where I work on machine learning methods for predicting brain age from T1 MRI. I learn every day different things about medical imaging, but I’m still very novice in this field.

My current goal is to parcellate each of cerebral cortex of my nifti MRIs into 148 cortical ROIs using Destrieux Atlas and compute the mean cortical thickness for each ROI and for each subject. I’ve found that the Freesurfer command mris_ca_label might help me to achieve this. But looking at the documentation, I see that the canonsurf parameter must correspond to a surface file whereas I have only volume file at my disposal. I’ve found that the command mri_vol2surf could help me to get surface files from nifti MRIs, but I don’t understand what type of output I can get with it.

I think my goal is to obtain for each subject a surface file, a label file and a thickness file. Therefore I would be able to compute the mean cortical thickness for each ROI and for each subject.

I would really benefit from any advice or explanation about this subject, thanks in advance.

Eventually, I found that the recon-all -all command can be the solution, although it’s very time-consuming.

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