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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
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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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