Registering dMRI streamlines to MNI with SPM

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1

Hello,

I am wanting to use the SPM toolbox to warp dwi streamline tractographs. My current pipeline would be to:

  1. coregister t1 to b0
  2. register b0-registered t1 to MNI152 with SPM and get warp field
  3. apply warp field to .trk with scilpy’s scil_apply_transform_to_tractogram.py

Has anyone tried doing this? Also, the SPM deformation / warp field is 86x86x86x3, while the t1 image is 256x256x256, why is this the case? The MNI space to which the t1 is being deformed I don’t think is 86x86x86.

Thanks in advance!
Hank

2

Hi @hankghgold,

Not a direct answer to your question but you might find this tutorial helpful: DIPY — dipy 1.8.0 documentation

Hard to say without knowing how you did the registration and without knowing the dimensions of the b0.

Most DWI processing pipelines (e.g., QSIPrep) will give you DWI images in the space of your T1, so I’m not sure if the first registration is necessary. In any case, if you need to calculate two registrations I would make sure to not to apply two registrations, but rather apply a single one that is the multiplication of the two transformations to reduce data interpolation.

Best,
Steven

3

Hi Steven,

Thank you for the quick response! That tutorial is helpful. I tried first registering the un-altered t1 to mni with spm, the unaltered t1 is 256x256x256. I can’t find anything indicating MNI spaces have the dimensions of 86x86x86. I do wonder, I know SPM uses a modified MNI 152 space.

Best,
Hank