Add code to preprocess anatomy/fieldmap data

shimming-toolbox / b0-fieldmap-realistic-simulation

Optimization of shim coil layout placement using simulated B0 and B1 maps constructed from segmented MRI scans of the head and full spine region. This is a collaboration between NeuroPoly Lab (Montreal) and MGH Martinos Center (Boston).

MIT License

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Add code to preprocess anatomy/fieldmap data #3

Open jcohenadad opened 1 month ago

jcohenadad commented 1 month ago

To make sure we can all reproduce the results of this project, i suggest we put on GH the code that:

fetches a specific version of the dataset
loops through all subjects
perform whatever preprocessing is needed (eg: smoothing of masks, related to #1 ), cropping (eg: based on vertebral labels to only keep the brain + c-spine)
perform processing (eg: getting susceptibilty and fieldmap), related #1
run shim layout optimization model @govish

mathieuboudreau commented 1 week ago

Steps 1-4 listed are done as of v1.1 - https://github.com/shimming-toolbox/b0-fieldmap-realistic-simulation/tree/v1.1