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Thank you for the suggestion. Is it possible to just calculate certain sub-field volumes such as the head body and tail as opposed to all of them?

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

On Mon, Apr 1, 2019 at 1:22 PM Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:

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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

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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*

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