eddy cmdline choice

[yibeichan]

there are two cmdline choices in eddy, either eddy_openmp or eddy_cuda, which depend on the input use_cuda. @ghisvail, in your example here, you only used eddy. I also tried use eddy only when converting from nipyper to pydra with our converter, but it doesn't work. Do you have any ideas about how we should deal with eddy_openmp and eddy_cuda? Thank you!

[yibeichan]

never mind, I think eddy works; Dorota and I just found out that my test data has some problems, not the problem from cmdline

[ghisvail]

Yes, it's a complicated story 😅

Prior to the new conda distribution of FSL, there used to be eddy, eddy_openmp and eddy_cuda${CUDA_VERSION}. With eddy becoming deprecated at some point.

With the new conda distribution, eddy_openmp was renamed to eddy_cpu, eddy_cuda${CUDA_VERSION} is still the same, and eddy is now the recommended entypoint which just dispatches to the CPU or CUDA version based on some runtime checks.

[ghisvail]

I focused on the new Conda version (version 6.0.6 onwards) hence the difference with the nipype interface.

[yibeichan]

okay, sounds good. I'm testing the code with some example data (I asked chatgpt to generate the whole set of test files) but got errors with reading epi_index/bvecs.scheme. since I can't push my code because of this issue #51 so I don't actually know whether it's something wrong with the code (I can't show you either) or with the example data. I'll fix the data quota first then come back to this one