Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images to further exclude the lesion voxels on the DTI maps (and to calculate DTI metrics within the lesions too). Using mri_vol2vol command I think I am missing something because I tried with the registration file produced by bbregister (through tracula) but the result does not look correct. I have the lesion mask in the freesurfer space that I can overlay on brainmask or dtifit_FA.nii on freeview and it seems correctly registered on both. The command I am running is: mri_vol2vol --mov recons_dir/subj1/dmri/lowb.nii.gz --targ /lesion_mask/subj1/lesion_WM.nii.gz --interp nearest --o /lesion_mask/subj1/lesion_WM_vol2vol.nii.gz --reg recons_dir/subj1/dmri/xfms/anatorig2diff.bbr.dat --no-save-reg --inv
And then when I open lesion_WM_vol2vol.nii.gz in freeview, the voxel size is the same as the DTI images, but the lesions are not at the same place.
On the mailing list I have also seen other options but I am not sure if they would be appropriate? I have seen mri_label2vol command where I could set the fill threshold parameter but it does not solve the problem of the registration file? also mri_convert And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension as the diffusion space?
Thanks a lot Best Celine