[ENH] Improve the crop_nifti
#1430
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AliceJoubert
approved these changes
Feb 14, 2025
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Thanks for the work @NicolasGensollen ! LGTM, I just have 2 comments about the NiftiImage class
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Thanks for the review @AliceJoubert ! |
Yes @NicolasGensollen it looks good to me now ! |
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Following #1426, this PR proposes to improve the
crop_niftifunction.Currently the function behaves in a very specific way, by cropping the provided image with a hardcoded bounding box that we defined for a specific use case (T1 images with MNI reference template). Therefore, I think the name is misleading and we could make use of a more generic function.
This PR proposes to make
crop_niftimore generic by letting users provide both the bounding box and the reference image. If no bounding box is provided, then no cropping is performed. If no reference image is provided, the input image is used as a reference. In other wordscrop_nifti(img)with no other argument is the identity function.The old
crop_niftihas been renamedcrop_nifti_using_t1_mni_templateand is nothing more than a partial function on the newcrop_nifti, calling it with the MNI_BBOX and the MNI cropped template.Implementation details: I introduced two classes called
NiftiImageandNiftiImage3Dwhich behave as wrappers around a path to a nifti image. I'm still unsure whether we should keep them or not, but I think it could help us reduce boilerplate code we have in various places to check that a nifti is 3D, or that a nifti file exists, and so on.