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I thought a solution like this might work but there seems to be an issue reading in the file.
I tried using mri_segstats on the .mgz file like this to create the stats file as this is what I do for my dt_recon results however it doesn't seem to work when I just want the volume stats?
mri_segstats --seg /Volumes/DANIEL/freesurf/${cond}.${subj}.long.base_${subj}/mri/lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz --ctab /Applications/freesurfer_dev/FreeSurferColorLUT.txt --id 226 --id 231 --id 232 --sum ${SUBJECTS_DIR}/${cond}.${subj}/stats/lhipp_volume.stats
Any ideas on how to make this work or a potential other work around.
Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298