Hi Anastasia Thanks for your answer. I think I am missing something because I tried with this registration file 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 seemed 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 sieze is the same as the DTI images, but the lesions are not at the same place. That is why I thought I had picked the wrong registration file...? Celine > > Hi Celine - If the lesion mask is already in the space of the freesurfer > recon, you can pass to mri_vol2vol the dmri/xfms/anatorig2diff.bbr.dat > transform. That's the one generated by bbregister for the > anatomical-diffusion registration. > > Hope this helps, > a.y > > On Thu, 13 Feb 2014, Celine Louapre wrote: > >> 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 (that have been processed with tracula) to further >> exclude the lesion voxels on the DTI maps. >> To do so I have found several possibilities on the mailing list but I am >> not sure about which one is appropriate. >> I have tried: >> mri_convert but I am not sure about which resampling method to use. The >> nearest voxel miss quite a few lesions. >> I have also seen the command mri_vol2vol: >> mri_vol2vol --mov /subject/dmri/lowb.nii.gz --targ lesion_mask.nii.gz >> --inv --interp nearest --o lesion_mask_resampled.nii.gz --reg >> /dmri/xfms/? >> --no-save-reg >> I don't know what registration file to use in that case? >> >> I have also seen mri_label2vol command where I could set the fill >> threshold parameter but I am not sure again about the registration file >> to >> use. >> >> And eventually I also saw this command: >> mri_mask but I guess that the mask volume needs to be in the same >> dimension than the diffusion space? >> >> Thanks a lot in advance for your help >> Best >> Celine >> _______________________________________________ >> 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
