Fix atlas handling and transform file issues in bundle_seg

[gagnonanthony]

When we changed how to provide a local copy of the bundle_seg atlas, we did not modify the path where the subworkflow fetches the files.

We don't have test data to include in the test suite, but I did try it locally, and everything runs smoothly.

[gagnonanthony]

We should discuss what to do with the transform files as output from the registration scripts. As shown here, we might need to access only one of the two transformation files from the output channel. I'm not sure this is the best way to do it, because

1. It is not intuitive to extract (flatten, then back to list, then map).
2. It won't work if the user select rigid transform, since only one transformation file will be outputted.

I think we should separate the output files in individual channels. From my experience, this also facilitates the pipeline/subworkflows creation process. What do you think @AlexVCaron, @ThoumyreStanislas, @arnaudbore, @Manonedde ?

[AlexVCaron]

Go for it ! I do agree it will make things easier. We implemented it that way to facilitate chaining transforms and prevent errors, but it just makes things harder and obscure.

[gagnonanthony]

I've updated the registration scripts @AlexVCaron. However, I struggle to update the snap of synthregistration (I do not have 20GB of RAM available...). Could you update them?

[AlexVCaron]

I've updated the registration scripts @AlexVCaron. However, I struggle to update the snap of synthregistration (I do not have 20GB of RAM available...). Could you update them?

I'm on that !

[AlexVCaron]

@rerun-checks

[AlexVCaron]

The tests pass ! But version files don't match for synthseg in the subworkflow ... so close, yet still not there yet 😅

[AlexVCaron]

The tests pass ! But version files don't match for synthseg in the subworkflow ... so close, yet still not there yet 😅

FYI, I assume you know this already, you can fake the version file at the correct versions and use md5sum to get the encoded descriptor.

[AlexVCaron]

Once version files are fixed, and the few comments I left here, this will be GTG ! 🚢

[AlexVCaron]

GTG on my end, once the tests pass 🤟🏻 Great job !