Hi Gregorio,

you need to transform the *mgz output images accordingy to NIFTIs images. Here is some exemplary shell code for the left hemisphere - operating in a subject's mri folder, using the FS6.0 type of aggregation (if you used FS7.1, you might to adapt the v-snippet in the filename):

cd <to.some.mri.folder>

mkdir test

cp lh.hippoAmygLabels-T1.v21.FS60.mgz test/left_discreteLabels.mgz

cp nu.mgz test

cp aparc+aseg.mgz test

cd test

mri_convert --resample_type nearest --out_orientation RSA left_discreteLabels.mgz left_discreteLabels.nii.gz
mri_convert --resample_type nearest --out_orientation RSA aparc+aseg.mgz aparc+aseg.nii.gz

mri_convert --resample_type nearest --out_orientation RSA --reslice_like left_discreteLabels.mgz nu.mgz nu_left.nii.gz

mri_convert --resample_type nearest --out_orientation RSA --reslice_like left_discreteLabels.mgz aparc+aseg.mgz aparc+aseg_highres_L.nii.gz

Then try to overlay the nu_left.nii.gz with the left_discreteLabels.nii.gz in some viewer (e. g. MRICron, or freeview).

By extracting only the voxels with a specific regional code you could create masks for your analyses, letting aside

the problem of the usually very coarse fMRI resolution.

Best,

Philipp

Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Borghi, G. (Gregorio) <gregorio.borghi@donders.ru.nl>
Gesendet: Montag, 12. April 2021 19:23
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Use Hippocampal segmentation sub-nuclei on other brain softwares

External Email - Use Caution

Dear All,

I have been stuck on this issue for quite some time. What I am trying to do is running a segmentation on both amygdala and hippocampus, and then to look at the different activation of the segmented sub-fields of both structures during a social-emotional task. However, despite my efforts I have not been able to find a way for translating either the segmented output files to bring them in a format that can be used by R, FSL, or SPM. Is there anyone who might have an answer on how to do that? Or is there a function in freesurfer that provides the list of voxel coordinates per volume for each hippocampal and amygdala subfields?

Kind regards,

Gregorio Borghi