Dear Alex,

As explained in the wiki, if you run the module on a FreeSurfer processed subject, the output will be in the subject’s mri directory, and will be called: hypothalamic_subunits_seg.v1.mgz

So you could run something like:

cd $SUBJECTS_DIR/<SUBJECT_NAME>/mri

freeview nu.mgz hypothalamic_subunits_seg.v1.mgz

If you ran the module on a raw t1 scan, then the output will be wherever you specified with the flag -o

Kind regards,

Eugenio

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 "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" <ladn@email.gwu.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, March 16, 2021 at 23:22
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hypothalamus segmentation output

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Dear Freesurfer experts, 

Hope that you all are well and stay safe. 

I would like some help figuring out the code to open the output for the hypothalamus segmentation (via freeview). Does anyone have this info? I didn't find it on the website. 

Thank you so much! 

All the best, 

Alex