Hi,
I am trying to convert the ribbon (amongst other mgz files) from a freesurfer run to the native space ANALYZE file I initially imported into freesurfer. I need to do this to create a cortical ribbon mask as a pre-processing step for normalization (with another package). However, every mgz file in the mri/ folder, after conversion, has a slightly different spatial distribution after conversion. Although, when I convert 001.mgz and rawavg.mgz the resultant image matches the image I imported exactly. By spatial distribution I mean, minor cortical fold shifts (up down, left right) and individual minor rotations in the cortical folds, some minor internal translations.
I think I tracked the problem down to the conform step, when rawavg.mgz gets conformed (mri_convert --conform) to 1x1x1mm and saved as orig.mgz.
I need to ensure a spatially correct cortical ribbon in the native space data. Is there any way to un-conform ? or some way to say, convert orig.mgz BACK to rawavg.mgz?
For reference, this is the command I am using to convert .mgz to ANALYZE (.hdr, .img): mri_convert --out_orientation LSP -rl native_mri.img orig.mgz converted_native_mri.img
I would really appreciate any help as this is my LAST roadblock!
Thanks in advance, -Arthur