How to save brain structural edited masks (segment edited) in nifti for freesurfer use?

Hi! I automatically generated structural brain masks with the purpose of using FreeSurfer. The masks need some editing, and I used Slicer Segment Editor for it (opened mask as label > imported labelmap as segmentation > add T1 as master volume > edited masks). However, I couldn’t save it as a nifti, so I saved as nrrd and later converted it to nifti. It didn’t work. How can I save my edited mask (in nifti) in order to use them for freesurfer? Do I have to convert the labelmap in something else?


You can use the Export to file feature in Segment Editor module. NIFTI export is available in the current Slicer Stable Release.