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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Borghi, G. (Gregorio)
<gregorio.bor...@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
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