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DevelopmentalImagingMCRI / MCRIBS

Surface version of the M-CRIB atlases.
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Misalignment Issues with mcribs-Generated Surfaces in nibabies #14

Open yanbin-niu opened 2 months ago

yanbin-niu commented 2 months ago

Hello!

I’m using nibabies with the mcribs flag to process an edited aseg file. mcribs generates surface files based on the aseg provided, and the results look better than those from infant surfer! Thank you for creating such a great tool! Recently, I am trying to map a volume file in native space (.nii.gz) to a surface (fsaverage), but I’ve encountered a strange misalignment issue with the surface directions. Here’s what I tried:

I used mris_convert to convert surface into .surf.gii files. For example: mris_convert rh.midthickness rh.midthickness.surf.gii . This generated a surface with incorrect directiona (see below), and this only happens with surfaces generated by mcribs and regular infant freesurfer surface files have no issues. image

I’m wondering those questions:

  1. is it considered a bug or did I miss anything or use mcribs incorrectly?
  2. Why do mcribs-generated surfaces look fine with freesurfer, but show directional issues when converted to gifti file?
  3. I also use lh.sphere.reg2 and rh.sphere.reg2 that generated by mcribs to convert a .mgh file from native space into fsaverage, but it looks not right after conversion. I am wondering maybe I used wrong fsaverage to overlay. I found one here from your github: lib/fsaverage, but looks not right as well: image

    so, which fsaverage does .sphere.reg2 generated by mcribs map to ?