If you look in the recon-all.log file for any subject, you will see a mri_aparc2aseg command line. YOu can use that specifying your annot and the new output name.

On 8/1/2019 4:58 PM, Mahshid Fouladivanda wrote:

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Dear experts,

I have a segmentation file of all the tissues in the brain and the ribbon file which were extracted by another toolbox rather than freesurfer. Also, I have created the annotation file using "write_annotation.m". Now, I wanna create a parcellation file based on the segmentation and annotation files using "mri_aparc2aseg" in freesurfer. Bellow is the command I entered in the terminal and extract the parcels:

mri_aparc2aseg --s subject name --annot annotation name --o output name

and I used the segmentation file as the "aseg.mgz" for the above command. Now, I am wondered that do I select the right aseg file or not??

Any help would be appreciated.

Regards,

Mahshid
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