Julien Cohen-Adad

@andreanne-lemay if i understand correctly, what you would like to do is bring image A into the voxel-coordinate space of image B. If that's what you want to do, then...

regardless, we should clarify the documentation for `sct_crop_image -ref`, i.e. `-ref` is supposed to be a binary image, with an object (e.g. a box), that defines the bounding box for...

> I thought the cropping you are describing was with the option -m Binary mask that will be used to extract bounding box for cropping the image. Has priority over...

> Maybe as a quick fix, the code from `sct_register_multimodal -identity 1` could be reused for `sct_crop_image -ref`? yes, this sounds like a reasonable approach. For now you have a...

added priority flag because the change proposed here will break compatibility with previous CLI

> Just to check... As per https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/1192, if we're updating the spinal level files, then we would also have to update the cord file too, no? I don't think so,...

> I modified some parts of this script in order to it fits the dcm-zurich dataset. It looks like this script is modified entirely (not only "parts" of it) see...

Also, please make sure to always link PRs with existing issues (I suspect https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4119 is related)

> Or, even better, not creating a PR at all. It's okay to work just from a branch without necessarily opening a PR if you are doing experimental work I...

> Sorry for the confusion, I think we can delete this PR. No, one of the purpose of the PR is to _see_ the code. In your issue, you are...