External Email - Use Caution
How about quantifyHAsubregions.sh? Cheers, /E
-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Daniel Callow ddcc2442@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 April 2019 at 13:19 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] segmentHA_T1.sh
External Email - Use Caution 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.commailto:ddcc2442@gmail.com 443-254-6298