Registration of tractogram to MNI152 space

[FEHildesheim]

Hello,

I would like to register my DWI tractogram (as generated by tckgen) into MNI152 space, so that in a next step I can overlay the AAL-atlas (which is in MNI152 space) on the tractogram to do my ROI-based analyses.

I tried the following:

1. register mean B0 DWI image to brain-extracted T1w image (using fsl FLIRT)
2. register T1w image (with B0 DWI registered to it in previous step) to MNI152 space (using fsl FNIRT)
3. create inverse warp of both files created in step 1 and 2 (using fsl invwarp)

The idea was to bring the MNI152 template in my individual subject’s DWI space. However, something is going wrong…

I would be very happy and thankful for some advice on how to correctly bring my DWI tractogram in MNI152 space.

Thank you,
Franziska

[maxpietsch]

Have you seen the wiki entries about image registration?

Registration: using transformations generated from other packages

The mrtransform allows the spatial transformation of images when provided with a suitable linear or nonlinear transformation (“warp”). For linear transformations, MRtrix3 uses homogeneous transformation matrices stored as plain text. These can be converted from FSL and ITK-based (plain text) convention with the command transformconvert. The MRtrix3 tools expect nonlinear transformations in an image format where each voxel defines the scanner space location in the other image. This transformatio…

Since you’re using FSL tools, I’d suggest you convert the FSL transformations to an MRtrix warp. You’ll need the transformations that bring the MNI152 template to the dMRI space. Once that works, you should be able to apply the same warp to the tractogram which transforms it to MNI152 space. This is all shown in more detail in the above link.

[FEHildesheim]

Great, thank you very much! It worked out!