External Email - Use Caution
Dear Freesurfer developers,
A collaborator shared with me Freesurfer outputs, but I would like to some analyses requiring the scans in NIFTI format. I understand mri_convert should do the trick for this, though I was wondering whether I should use "orig.mgz" or "T1.mgz" to convert back to the original T1 NIFTI files.
Many thanks, Colleen
Hi Colleen
it depends on what you want to do. The T1.mgz probably isn't the correct volume to use in any case. The orig.mgz is close to the raw data (e.g. it has a skull in it and has not been bias corrected). If you want a skull-stripped, bias-corrected version you could use either the norm.mgz (gently bias corrected so it still shows subcortical boundaries) or the brain.mgz (aggressively bias corrected, may wash out e.g. thalamus and pallidum).
cheers Bruce
On Mon, 30 Apr 2018, C.P.E. Rollins wrote:
External Email - Use CautionDear Freesurfer developers,
A collaborator shared with me Freesurfer outputs, but I would like to some analyses requiring the scans in NIFTI format. I understand mri_convert should do the trick for this, though I was wondering whether I should use "orig.mgz" or "T1.mgz" to convert back to the original T1 NIFTI files.
Many thanks, Colleen
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Bruce Fischl -
C.P.E. Rollins