Transform mask data if orientation does not match volume, fixes #346

[LukasNickel]

Minimal addition to the code to fix the issue, that the volume and mask data have different orientations.

I avoided ToCanonical and instead only transform the mask data to match the volume.
After trying to implement the transform myself, I decided the safest way is probably to use the nibabel functionality directly. Torchio unfortunately only includes the transformation to canonical coordinates as far as I can tell...

Should be working fine, but I did not really test it much yet, which is why this is marked as draft. Hopefully I have the time for that on monday.

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[eigenvivek]

Hi @LukasNickel thanks a bunch for the PR. Looks good to me!

To properly merge it, the changes have to be written into notebook (see the dev guide). If that's cumbersome, I can push those changes to this branch sometime soon.

[LukasNickel]

Hi @LukasNickel thanks a bunch for the PR. Looks good to me!

To properly merge it, the changes have to be written into notebook (see the dev guide). If that's cumbersome, I can push those changes to this branch sometime soon.

I will have a look, just ran out of time on friday.

Although I have to admit, I initially misunderstood the purpose of the notebooks.
Would have assumed that the API doc is autogenerated from the code and the notebook content matters only for the "Tutorials"

Edit: OH, I had it backwards! You develop in the notebook and export that. That is both pretty neat (although I am undecided on whether its a net positive) and not really clear from the README imo.

[LukasNickel]

Turns out I completely skipped over the autogenerated comment in the code.
I was about to write how that might be a good idea to add lol.

There might still be a benefit of making the text in the README clearer, but I would say its 90% on me here and the description is mostly fine.
Just a niche thing to see literate programming in the wild and the autocorrect in my brain did not pick it up, mea culpa!

[eigenvivek]

Hi @LukasNickel thanks for the PR and the feedback. Looks good to me! I updated the README to be clearer.

[eigenvivek]

Closes #346