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Hi freesurfer experts,
I'm trying to extract mean FA values (dti_FA.nii.gz) using a segmentation
volume (parc2502dwi.nii.gz) and the corresponding color table with:
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
# extract FA
mri_segstats \
--seg mri/parc2502dwi.nii.gz \
--ctab colortable.txt \
--i $dtipath/$subj/dti_FA.nii.gz \
--excludeid 0 \
--sum ../FA/${subj}_fa.stats
cd ../
fi
done
The color table has 297 parcels specified but the summary statistics file only
includes 38 regions. This is due to zero values in the other regions, I assume.
Both (dti_FA and parc2502dwi) are perfectly co-registered.
Not providing a color table results in 1234 regions being read out.
Am I missing an argument in my command?
Or is there anything else that is obviously wrong?
I would be very glad for some hints!
Thanks,
Steph
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