Dear Elizabeth, You command looks good to me. Did you visualize lh_Amyg_native.mgz with colormap=lookup table? Cheers, /Eugenio
Juan Eugenio Iglesias http://www.jeiglesias.com
On Aug 14, 2022, at 18:58, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
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Hi Freesurfer Developers,
I have segmented hippocampal/amygdala masks for my participants with the segmentHA_T1.sh script, but I am wanting to transform these masks into native space for analysis. I have tried using mri_convert (command below), however, this command gives me a binary mask rather than one containing all the segments. Is there an additional step I need to include to retain the information from the segmented data when transforming the mask?
mri_convert -rl rawavg.mgz -rt nearest lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz ./lh_Amyg_native.mgz
Many thanks, Elizabeth _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer