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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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