Did you check the registration? My guess is that the registration failed because the initial FSL registration failed. I've put a new version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/dt_recon it has a better initializer. Just copy it over the one in $FREESURFER_HOME/bin (make a backup of the original one though) On 2/25/19 1:50 PM, Daniel Callow wrote: > > External Email - Use Caution > > Hello freesurfer experts, > > I am running dt_recon with the following script > > dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i > /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/image000001.dcm > --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}. > > > and mri_vol2vol to get the wmparc and aseg.mgz files in my lowb space > with the script below > > 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, > > *Daniel Callow* > /PhD Student, Neuroscience and Cognitive Science/ > Exercise for Brain Health Lab > University of Maryland, College Park > _ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>_ > 443-254-6298 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
