Avoid re-resampling unnecesary files

[jan-petr]

Description

The step 8 Resample to standard space (line 430) is run also when FLAIR, rT1, rcT1 are missing in the standard space. Which doesn't make sense as these are always removed during cleaning. So this has to be rewritten while focusing on the PV_PGM files. We should merge #1543 and #1588 before continuing work on this.

HENK: Not sure what you mean by this. I had to search. So you mean xASL_module_Structural-> step 8.
Now I get what you mean. The answer is: we need these standard space copies for the visual QC JPGs created in step 10 Visual QC. E.g., we use FLAIR and rc1T1 to show the registration of FLAIR to T1w. We use rT1 to show the lesion filling.

We could improve this by creating the QC directly within the wrapper that creates it's output, but this is tricky for the structural module because of the interdependence between the FLAIR and T1w NIfTIs/images. Another thing we could do is to have an automatic way to transform images to standard space if they are requested but only exist in native space. This would be nice as a fail-safe, but less efficient perhaps then transforming multiple images in one go.

Tasks

• Fix xyz in function xASL_[abc]_...

How to test

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Release notes

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