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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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Field Map Masks for Brain + C-Spine Images #2

Open Govish opened 3 months ago

Govish commented 3 months ago

Hi guys! I took a peek at the masks you sent over, and it looks like they include just the brain. Would it be possible to get masks that include all anatomy requiring shimming (i.e. brain + c-spine, etc.)?

Thanks! -Ishaan

CharlesPageot commented 3 months ago

Hi @Govish! Sorry for the wait. We have the whole spine segmented for the dataset. I will generate the masks. Just to be sure, you want a single mask for each of the subject that include brain + spine ?

Govish commented 2 months ago

Hi Charles! Sorry for the radio silence on my end! I just got a chance to go through the masks you sent that included the spine, and they're a lot closer to what we're looking for. However, it looks like they include the whole spine. Would it be possible to get masks that just include the brain + C-spine (C1-C7)?

Thanks for your continued help and support! -Ishaan

Govish commented 2 months ago

^ In chatting with my PI's actually, would getting all segmented tissue maps be possible? (e.g. having separate masks for brain, all vertebrae of the spine, lungs, etc.)

CharlesPageot commented 2 months ago

Yeah, for sure, we have the combined label maps. The vertebrae are currently all under the same class (same thing for the discs). Do you need them to be all separate (i.e. one label for C3, another one for C4 etc) ?

Govish commented 2 months ago

That would be great! Apologies for the late reply!

jcohenadad commented 1 month ago

@Govish is this issue solved?

Govish commented 1 month ago

Not yet (at least I don’t have individual tissue maps yet)—I may have missed an email/message however. Thanks for all the help!

jcohenadad commented 1 month ago

Will be addressed in #1 once we share the source data (ie: mask of each tissue)