New Extension mp2rageBackgroundSuppression

[SamBrenny]

New extension

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If you have any questions or concerns let us know

[jcfr]

Thanks for the contribution 🙏

After a cursory review, here are some issues you should consider addressing:

• Improve README harellab/SlicerUHFMRTools#1
• Cleanup files harellab/SlicerUHFMRTools#2
• Make sure Python module mp2rage_contrasts is packaged and distributed harellab/SlicerUHFMRTools#3
• Cleanup scripted module removing unused code harellab/SlicerUHFMRTools#4

Last, similarly to the SlicerFreeSurfer extension I am wondering if this extension should be called SlicerMP2RAGE ?

Or since this work seems to be done in the context of a larger initiative¹ related deep brain stimulation (DBS), would it be sensible to add a new module to the SlicerNetstim extension (and may be having it renamed SlicerDeepBrainSimulation ?)

cc: @pieper @lassoan

Related

• https://dbsguidedocs.readthedocs.io
• https://github.com/wafiqsyed/dbsGuideDocs

Footnotes

1. https://movementdisorderslab.umn.edu/projects/udall-study ↩

[hbraunDSP]

Thanks! We'll get to work on the issues you submitted. Regarding changing the name, I tentatively support moving to SlicerMP2RAGE. There is nothing DBS-specific about this feature, so I don't want to make it part of NetStim -- MP2RAGE is just a T1-weighted contrast, applicable anywhere a T1 image is needed but particularly useful at higher field strengths on Siemens scanners.

[jcfr]

I tentatively support moving to SlicerMP2RAGE

cc: @pieper @lassoan

[pieper]

Having larger extensions that include a set of related modules is cleaner I think. It's easier for users to manage just one extension and it's easier for us as extension maintainers if there's an team that "owns" a topic and can decide what to include. Moving this into an existing extension would be preferred if there's a match.

[hbraunDSP]

I don't see a good match among the existing Slicer extensions, but feel free to suggest one if I missed it. We've addressed the issues @jcfr submitted; We'll change the extension name to SlicerMP2RAGE and any future MP2RAGE-related tools can be added to it.

[SamBrenny]

The Slicer extension mp2rageBackgroundSupression has been renamed to SlicerMP2RAGE and updated documentation. We believe this is ready to merge.

[hbraunDSP]

We'd like to get this merged, and as far as we know it's ready. Are there any changes you'd like us to make?

[pieper]

Looking again I have a couple more comments:

• I see you have a non-module file in this folder that should be in a subdirectory (like a Lib directory) so it won't be part of the module discovery process.
• The testing nrrd files in the repository are not a huge problem for a single tool like this, but generally they should be hosted another place, like in a release asset and the test should be configured to download them when they are needed (e.g. so that a user of the module could optionally run the test but the test data is not installed for every user).

[pieper]

Not sure why the lint check failed. https://github.com/Slicer/ExtensionsIndex/actions/runs/8209333331/job/22491632783?pr=1983

Doesn't look like a problem though, so I'll go ahead and merge this.