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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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