If you just need the aseg in nii.gz format, then you can

mri_convert aseg.mgz aseg.nii.gz

If you need a particular seg in its own file, then you can

mri_binarize --i aseg.mgz --match 17 --o left-hippo.nii.gz

where 17 is from $FREESURFER_HOME/FreeSurferColorLUT.txt


On 5/2/18 5:47 AM, Otília wrote:

  

 

Hi to all FS users!

Sorry in advance if I'm cross-posting but after searching and trying some stuff I still can't figure out how to do this.

After all the processing in FS I would like to evaluate the labels (from each participant) in other software (aseg labels). I imagine I would need to binarize the label of each subject as masks or volumes, in .nii or some more common file type.

Do someone know how to do that?

Any help would be very much appreciated! Thank you!

Best regards,

Otília





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