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

External Email - Use Caution 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