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 > > > > > ------------------------------------------------------------------------ > Windows Live: Make it easier for your friends to see what you’re up to > on Facebook. Find out more. > <http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_facebook:082009> > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
