Trouble Creating .annot Files for Extracting Freesurfer Data

[RobertJirsaraie]

Hello @yetianmed,

Thank you for making this atlas available in volumetric space and in cifti format. I believe in order to extract freesurfer data, I need the surface files to be in .annot format, which I have done before using the following two commands as an example:

#Separate the CIFTI file into GIFTI files
wb_command -cifti-separate ${NII} COLUMN -label CORTEX_LEFT ${GII}

#Convert GIFTI files to FreeSurfer annotation files
mris_convert --annot ${GII} ${HCP} $PROJECT_DIR/freesurf_extract/lh.HCP-MMP1.annot

The issue I am running into is when creating the GIFTI file, I have to specify which hemisphere or subcortical region to extract from the .dlabel.nii files. It is clear how to do this for the cortical hemispheres, but not for the subcortical regions in this atlas. Ideally, I can extract all subcortical parcels into a single .annot file, but I am not sure if this is possible. Please let me know if you have done this before and whether you can have .annot files that you would be willing to share. Thanks again!

[catvasily]

Hello.
I have a somewhat related question. 
Freesurfer's .annot files are surface parcellations.

But we would like to generate volumetric parcellations, as defined by aseg.mgz files.

By default, Freesurfer's recon-all seem to return aseg.mgz for the Destrieux and Desikan-Killiany-Tourville (DKT) atlases:
aparc.a2009s+aseg.mgz
aparc.DKTatlas+aseg.mgz

Do you know how we can provide one of the Melbourne parcellations to FreeSurfer's recon-all in order to generate subject-specific aseg.mgz for the Melbourne atlas?
Thanks.