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Dear Haley,

The Matlab version of SynthSeg writes nifty files. You could run the FreeSurfer command to convert to mgz (and rename to aseg, along the way): mri_convert synthseg.nii.gz aseg.mgz

Now: I don’t know if it’s possible to simply replace FreeSurfer’s aseg.mgz by this new aseg.mgz and keep running from there. I’ll defer to Doug and Bruce (CCed) on that.

Cheers,

/Eugenio

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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu Date: Saturday, August 26, 2023 at 12:22 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Import Matlab SynthSeg labels to FS External Email - Use Caution

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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