dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}.

mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/wmparc.mgz --inv --interp nearest --o /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz --reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg

mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/aseg.mgz --inv --interp nearest --o $subj_dir/dtrecon/${subj}.${cond}./aseg2diff.nii.gz --reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg

However, one of my subjects shows a major issue with the mri_vol2vol registration (for most of the subject scans it seems to work no problem). When looking at the wmparc2diff.mgz I created, it is apparent that the registration of the wmparc to wmparc2diff space actually causes wmparc2diff.mgz to be further from the lowb than wmparc is (the brain is shifted severely to the right). This same registration issue occurs for aseg.mgz.

When I look at fa-tal.nii.gz it is poorly registered (again worse than FA overlayed on aseg or wmparc which happens to be pretty close without dt_recon). I assume this means there is an issue with the register.dat file for this subject?  If so is there any way to troubleshoot the issue and get a correct register.dat file from dt_recon?

For reference, the following commands and registration steps have worked for other subjects, as well as this same subject's scans under a different condition. At first glance there don't seem to be any specific issues with the anatomical or diffusion images before the registration attempt.

Any advice with troubleshooting would be greatly appreciated.

Best,