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Hello! freesurfer experts,I am running dt_recon and mri_vol2vol to obtain FA values of five corpus callosum (CC) sub-regions.
command 1, dt_recon --b bvals.dat bvecs.dat --i $TUTORIAL_DIR/$subj/DTI/00001.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon
command 2, mri_vol2vol --mov lowb.nii.gz \ --targ $SUBJECTS_DIR/$subj/mri/wmparc.mgz \
--inv --interp nearest --o $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
--reg register.dat --no-save-reg
Everything is OK after running the dt_recon command and the registration of all diffusion images with the anatomical data is good. However, some of my subjects show an issue with mri_vol2vol registration. When checking the wmparc2diff.mgz I created, it is apparent that surfaces of lh.white and rh.white are not accurately mismatched with the wmparc2diff.mgz, as showed in the following figure. Is there an error with my command about mri_vol2vol or a problem in other aspects? Any advice with troubleshooting would be greatly appreciated. Best Wishes Bo Tao M.D Student, Department of Radiology / Huaxi MR Research Center (HMRRC）West China Hospital of Sichuan University Chengdu City, 610041 P.R. China
