Weird Artifacts in Masks

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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Weird Artifacts in Masks #1

Open Govish opened 3 weeks ago

Govish commented 3 weeks ago

Hi guys, hope you're doing well!

We've been running into some issues with some artifacts in the mask--there seem to be some rough edges/bleeding that may not be accurately capturing only the target anatomy. The image you hopefully see below shows this detail on fieldmap_3.

We've been able to work around this issue by eroding the masks by 3-4 voxels, but a root-cause fix would be much appreciated. It's had been noticeably impacting the performance of the optimizer and validity of the results.

Thanks! -Ishaan

jcohenadad commented 6 days ago

@Govish sorry for the slow reply. Just to be sure: are you talking about the fieldmaps produced by our team and sent by @CharlesPageot within the context of our collaboration? If so, I would not use this repository to discuss that project. This repository is specifically about the susceptibility-to-fieldmap software. We should start a new repos (in this organization) and transfer this issue. In the meantime, @CharlesPageot can you please assist @Govish?

Govish commented 5 days ago

Yeah--I'm referring to the field maps sent over in the scope of our specific collaboration; and sounds good! Let me know where would be a good place to discuss this! However, I think this issue may be a bit more general than our specific collaboration—I’m not sure if some of these masking issues may persist with other field maps. Thanks!

jcohenadad commented 3 days ago

@CharlesPageot will write up a procedure to address this issue, but briefly:

@CharlesPageot share the source data (ie: masks output from TotalSeg) with @jcohenadad. Currently, data were sent as one package via onedrive. Approximate size: 5GB. @jcohenadad will put the data on OpenNeuro.
@CharlesPageot share code used to apply batch processing of: (i) mask to susceptibility (ii) susceptbility to fieldmap
@CharlesPageot describe procedure (on 3D slicer-- although not ideal bc not easily batchabe-- ideally: solution using CLI method, eg from FSL, ANTs, etc. for the purpose of smoothing 3D binary masks), and @jcohenadad review procedure
@Govish fill up the README with description of the purpose, and location of the data so we can all contribute
@Govish once procedure for smoothing mask is done, apply it and give feedback directly in this issue (screenshots, etc.)