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mattcieslak / MITTENS

A Python library for Analytic Tractography
BSD 2-Clause "Simplified" License
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Creating VoxelGraph #10

Open dubergonzoni opened 3 years ago

dubergonzoni commented 3 years ago

Please,

I'm trying to create a VoxelGraph graph, but I got an error creating the MITTEN object:

mitns = MITTENS(reconstruction="sub-01_dwi_merged.src.gz.odf.gqi.1.25.fib.gz") Unable to load real affine image

My fib.gz file is an ouput of the preprocessing with QSIPREP: https://qsiprep.readthedocs.io/en/latest/index.html Anny suggestion how to fix this problem? Am I using the wrong gqi file?

Thank you.

mattcieslak commented 3 years ago

Hi! No, you're using the correct file. The fib format doesn't have affines in it, so you have to provide an external nifti file. In the case of QSIPrep you can use path to the dwiref.nii.gz file as the argument for real_affine_image.

Also, you should make sure you're using the desc-preproc_*fib.gz images if you're using outputs from QSIPrep. The file name in your example looks like a temp file that gets created during the preprocessing workflow, not the final output.