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
On 9/27/16 3:14 PM, Sepeta, Leigh wrote:
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
<mailto:lsep...@childrensnational.org>
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