Hi all,

I am trying to bring my FreeSurfer brainmask into SPM and then to coregister it 
(along with some ROIs from FreeSurfer) to the same subject's mprage already 
processed (coregistered to functional data) in SPM. To do this, I used:

mri_convert brainmask.mgz brainmask.nii.gz (then used gunzip)

and then looked at the brainmask and mprage in SPM and they both seem to be 
oriented correctly (left is left, right is right for each one--using anatomical 
landmarks as the guide). However, in reading up on this topic, many people 
advise using commands like these (often with RAS) when converting mgz to nii:

 mri_convert --in_type mgz --out_type nii --out_orientation RAS  brainmask.mgz 
brainmask.nii.gz

OR

 mri_convert --out_orientation RAS  -rt nearest --reslice_like <reference.nii 
or reference.nii.gz> <input.mgz> <output.nii>

OR

mri_convert -rl rawavg.mgz -rt nearest brainmask.mgz brainmask.nii.gz


Are any of the options (-rl, RAS, etc) in the last 3 commands listed necessary 
when going between mgz/nii for freesurfer to spm analyses if you know that the 
mgz and nii files are in the same orientation?

Thank you,
Leigh


<mailto:lsep...@childrensnational.org>

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