I'm actually wondering the same thing re AAL to subject space - this is what I have been using:

spmregister - reg template to subject mri_label2vol - move AAL to subject space mri_segstats - pull in-volume stats using AAL in subject space mri_vol2surf - project AAL (subject space) to subject surface mris_anatomical stats - pull surface stats

Am I making that more complicated than it needs to be? What I'm most unsure about is whether the atlas should be projected to the template surface then moved to subject surface, or if it should be moved to subject space then projected to surface.

Thanks! Sara

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of pfotiad@nmr.mgh.harvard.edu [pfotiad@nmr.mgh.harvard.edu] Sent: Monday, February 29, 2016 18:37 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] AAL atlas question

Hi FS community,

I have recon-ed a set of subjects and I was interested in also obtaining structural info (cortical thickness, gray matter volume, surface area etc.) based on a different atlas than the ones FS is using, and in particular the AAL atlas.

I was wondering whether my approach would be the correct one or whether there is another (better and more accurate) approach:

1) Convert the AAL atlas into a surface (with mri_vol2surf) from the MNI space into the native subjects' space, 2) Use mris_anatomical_stats to calculate the structural stats

Sorry for the potentially trivial question, and thank you for your time!

Best, Panos

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