which ROIs are different?
On 2/22/19 5:39 PM, Winkelbeiner, Stephanie A wrote:
>
> External Email - Use Caution
>
> 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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