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Hi Haley
I'm not sure I understand how you ran SynthSeg in matlab, but we supply .m
files for reading/writing volumes (MRIread and MRIwrite). You probably want to
read in the existing aseg to get the header, then replace the data with the
segmentation you want and then write it out
Cheers
Bruce
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Haley O Higginbotham
Sent: Friday, August 25, 2023 11:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Import Matlab SynthSeg labels to FS
External Email - Use Caution
Hi,
I experienced issues with segmentation (exclusion of large portion of
cerebellum) and so used SynthSeg in Matlab (as the built-in mri_synthseg in
freesurfer wasn’t working on my computer) to create the segmentation. Does
anyone know how to import the resultant 3D categorical array containing the
labels back into freesurfer (for the sake of further manipulating it in
freeview and replacing the aseg file)?
Best,
Haley
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