How to obtain 28 bundles (pyAFQ) in standard space (MNI) as NIfTI files?

Software Support
1

Hello everyone,

I am currently using the pyAFQ (Python AFQ) toolkit to perform tractography and bundle segmentation on diffusion MRI data. I have successfully run the pipeline and obtained 28 major white matter bundles (e.g., CST, SLF, etc.) in individual subject space. Now, I would like to konw these 28 bundles as NIfTI files (e.g., binary masks or probability maps) in a standard space (e.g., MNI). Could i use the JHU white-matter tractography atlas as an alternative one?

Thank you in advance for your help!

2

Hi @zychen,

To get to MNI you can use tcknormalise — MRtrix 3.0 documentation.

To get a nifti probablity map you can use tckmap — MRtrix3 3.0 documentation, which can then be binarized to get a nifti mask.

Best,
Steven

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