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 (screenshot attached), 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. This same registration issue occurs for aseg.mgz.

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?

For reference, the following commands and registration steps have worked for other subjects, as well as this same subject's scans under another condition.

Any advice with troubleshooting would be greatly appreciated.

Best,