fMRI BOLD projection to native space of DTI data

Dear all,
I’m working with BOLD fMRI data and DTI data, after extracting the active brain areas from the BOLD data, I need to project them into the native space of the DTI data in order to generate a tractography guided by these ROIs, so how can I perform this projection step with MRtrix3 ?
I will appreciate any help, Thanks.


If you are running fMRI group analysis in a standard template (i.e. MNI), then you need to first insure proper co-registration between your DWI and fMRI native space. I suggest you move the undistorted fMRI image to match the undistorted DWI’s and not the other way around. This way you reduce the risk of messing around the b-matrix (see for more detail about this issue). Once this is done, make sure that you save the inverse and forward transformation matrices during the segmentation/normalization step. This way you will be able to reverse normalize (invert transform) your clusters of activation back to the native space.

If you are only running single subject fMRI analysis, then I suggest to only insure proper co-registration between the modalities.


Dear #Julien_J,
thank you a lot for your attention, actually I’m only running a single subject fMRI analysis, that’s why I find some difficulties, so I will try to only insure as you mention proper co-registration between the two modalities.
thanks again,

We have some related threads in the community that should get you going for nonlinear

and linear registration

Thanks a lot #maxpietsch this threads helped me so much to understand how I can solve my problem.