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I'm trying to create an fsl reg file that maps a dwi image to native anatomical space. 1. I used bbregister to create a reg file that maps the transformation from nodif to freesurfer's conformed space: bbregister --s sub001 --mov nodif.nii.gz --reg nodif2orig.dat --dti --init-fsl --fslmat nodif2orig.mat 2. then I aligned my dwi images to orig.mgz using the reg file from step 1 mri_vol2vol --fstarg --reg nodif2orig.dat --mov dwidata.nii --o dwi-in-freesurfer.nii 3. finally I mapped dwi-in-freesurfer image to native anatomical space mri_vol2vol --target mri/rawavg.mgz --regheader --mov dwi-in-freesurfer.nii --o dwi-in-rawavg.nii However I only get the registration file nodif2orig.mat, which only maps the nodif to freesurfer space? How can I get an fsl.mat for the transformation from freesurfer to native space? mri_vol2vol has no flag to output an fsl-type registration file. Best regards, Sam
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