Have you solved the mismatch problem yet? I meet the same problem when I do co-registration (register DTI image to T1 image of the same subject).
I firstly do recon-all with T1 image, it will transfer T1 image to Talairach space, I named it
flirt -in DTI.nii.gz -ref t1_freesurfer.nii.gz -out DTI_flirtto_t1_freesurfer_tmp.nii.gz -omat DTI_flirtto_t1_freesurfer_tmp.mat -dof 6
flirt -in DTI.nii.gz -ref t1_freesufer.nii.gz -out DTI_flirtto_t1_freesurfer.nii.gz -init DTI_flirtto_t1_freesurfer_tmp.mat -omat DTI_flirtto_t1_freesurfer.mat -dof 6
transformconvert DTI_flirtto_t1_freesurfer.mat DTI.nii.gz t1_freesurfer.nii.gz flirt_import DTI_flirtto_t1_freesurfer_mrtrixformat.txt
mrtransform DTI.nii.gz -linear DTI_flirtto_t1_freesurfer_mrtrixformat.txt DTI_in_t1_freesurfer.nii.gz
However, The result:
Then I tried to use epi_reg (a script designed to register EPI images (typically functional or diffusion) to structural (e.g. T1-weighted) images) :
It seems works, but the outpur file is extremely large( original DTI->61.8 MB , output DTI->519.4 MB ),which brings a lot of pressure when I do fiber tracking. So I have to give up this method.
Finally, I find dt_recon will register the current diffusion data to the structural data in its process. As announced by FreeSurfer, Input the bvalue and direction information using bvec and bval text files with the same format as the files used in FSL diffusion processing.
It works. Register DTI image to T1 image in(talairach ? MNI305) space. In fact, I’m not sure it is talairach or MNI 305 as FreeSurfer announced.
dt_recon, I have to run
recon-all command, which takes more than 10 hours with even my machine is quite nice (8 CPU cores and Titan Graphic Cards).
I sincerely hope Mrtrix developers can provide some functions on intra-subject registraion, registration from functional/diffusion image to structual image. It will really be very convenience for the users.