I believe the problem is that they live in different voxel spaces (Doug, can you please clarify?)

Cheers,

/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 Marcel Heers <marcel.heers@gmail.com>
Reply-To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 4 December 2019 at 17:10
To: "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] hippocampal subfields as masks for mri_segstats

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Dear all, (dear Eugenio),

I would like to use hippocampal subfields as masks for mri_segstats to retrieve intensity values. I am having problems loading the subfields file although it works fine with aseg.mgz.

Does  anyone know the cause?

Thank you in advance!

Best regards

Marcel

mri_segstats --seg $SUBJECTS_DIR/test/mri/aseg.mgz --ctab-default --sum output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz

mri_segstats --seg $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz --sum output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz

ERROR: loading $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz