You do not need to specify that. In fact, you should not because it may mess up the orientation. You do not need to add any special arguments to mri_convert. You can also specify .nii instead of .nii.gz

Hi all,

Sorry to re-post:

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

 

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