I've just created a new wiki to describe how to do this:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Guang Zeng wrote:
Hi, there,
I used FreeSurfer pipeline to study a subject, I convert my .nii file to .mgz file, and then send it to FreeSurfer pipeline.Everything works well. Now I want to convert the wmparc.mgz back to the space that the original volume was.
I tried two command mri_covert wmparc.mgz -rl orig.nii new.nii
and mri_vol2vol --mov wmparc.mgz --targ orig.nii --regheader --o new.ii
Both of them gave me the same problem. My original volume is :
qform_name *Aligned Anat* qform_code 2 qto_xyz:1 -1.198313 -0.049354 0.044215 94.332878 qto_xyz:2 -0.041108 1.237333 0.172261 -131.942123 qto_xyz:3 0.048546 -0.170504 1.237284 -105.448372 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient *Right-to-Left* qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name *Aligned Anat* sform_code 2 sto_xyz:1 -1.198313 -0.049354 0.044217 94.332878 sto_xyz:2 -0.041108 1.237333 0.172261 -131.942108 sto_xyz:3 0.048547 -0.170504 1.237284 -105.448372 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient *Right-to-Left* sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior
Now the new resampled volume is:
qform_name *Scanner Anat* qform_code 1 qto_xyz:1 1.198313 -0.049354 0.044217 -96.198837 qto_xyz:2 0.041108 1.237333 0.172261 -138.478333 qto_xyz:3 -0.048547 -0.170504 1.237284 -97.729370 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient *Left-to-Right* qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name *Scanner Anat* sform_code 1 sto_xyz:1 1.198313 -0.049354 0.044217 -96.198837 sto_xyz:2 0.041108 1.237333 0.172261 -138.478333 sto_xyz:3 -0.048547 -0.170504 1.237284 -97.729370 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient *Left-to-Right* sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior
When I use fslview to view these two volumes, their orientations were swapped. Could you help me fix this problems?
Thanks a lot!
Guang
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