New subject: mri_segstats and mris_anatomical_stats read out different # of rois

22 Feb 2019


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Hi Freesurfers,
I'm trying to read out GM and WM values from parcels (ROIs) but get a different amount of ROIs for GM and WM.
I use the following commands (embedded in a loop),
for GM
mris_anatomical_stats -mgz \
            -cortex label/lh.cortex.label \
            -f stats/lh.250.aparc.pial.stats \
            -b -a 250.aparc \
            -c label/colortable.ctab \
            $subject lh pial
and for WM
mri_segstats \
                --seg mri/vol250.lh.nii.gz \
                --ctab ../fsaverage/colortable.ctab \
                --i $dtipath/$subj/dti_FA.nii.gz \
                --excludeid 0 \
                --empty \
                --sum stats/${subj}_fa_lh.stats
where "../fsaverage/colortable.ctab" has 299 labels and "mri/vol250.lh.nii.gz" is the segmented image that was extended 2mm into the WM and registered to the DTI image.
Is it possible that these two commands read out different amounts of ROIs?
And is there a reason why the -c flag in mris_anatomical_stats doesn't save the colortable for each subject?
I would be very grateful for some help!
Thanks,
Stephanie
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