Hi Gabriel, don't use the ASegStatsLUT.txt ctab file. It will only report the volumes of structure in the ctab, and that ctab does not have the WM parcellations. You can use FreeSurferColotLUT.txt instead. When you use --empty, this will report on *everything* in the ctab, which will probably be overwhelming. If you run it without --empty, then some subjects may have a different number of structures. The only alternative is to create your own ctab with only the structures you are interested in. doug

On 10/17/2012 02:36 PM, Gabriel Gonzalez Escamilla wrote:

Dear Freesurfer Experts

Sorry for many mail, but I'm working on may things at the time.

Apart from my corticalGM problems I'm trying to obtain the WM volumes from some regions in the apparc.annot such as precuneus, for this I'm using

mri_aparc2aseg --s MySubj --labelwm --annot aparc --o /root/trabajo/freesurfer/subjects/MySubj/mri/NEWaparc+aseg.mgz

to convert the apparc into a volume file, and then obtaining such voxels correponding to the asigned WM using:

mri_segstats --seg /root/trabajo/freesurfer/subjects/MySubj/mri/NEWaparc+aseg.mgz --sum /root/trabajo/freesurfer/subjects/MySUbj/stats/Newaparc+aseg.stats --pv /root/trabajo/freesurfer/subjects/MySubj/mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in /root/trabajo/freesurfer/subjectsMySubj/mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject MySubj

the problem is that even when it seems to work, some of the structures have no WM volume in the stat table, but they do have assigned voxels on the Newaparc+aseg (see attached image), Is there something I've been doing wrong? the command gives me the same results when I use the aparc+aseg.mgz created during recon-all process.

Can anyone guide me?

Best Regards, Gabriel

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