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.com

443-254-6298

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