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).
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Realistic segmentation of trachea and lung #18

Open sriosq opened 1 week ago

sriosq commented 1 week ago

After a short meeting with Maxime B. we have seen that the trachea segmentation lacks the bifurcation which connects the trachea with lungs. This would be very challenging to segment with a trained model but with the anatomical T1w image it is possible to discern.

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This may or may not be the reason why some subjects display fieldmap without the intensity peak around C7, but worth exploring the details.

A need for smoother lung segmentation as well as a revision of sharp discontinuities and wholes on the lung segmentation is also noted.

jcohenadad commented 1 week ago

We should do a couple of manual segs, and fine tune the existing model

sriosq commented 1 week ago

Update:

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There are some pockets of "lung"' out of place. Smoothing out the trachae segmentation now.

sriosq commented 1 week ago

@evaalonsoortiz @mathieuboudreau This is the final smooth segmentation for db0_030.

final_in_db0_030_segs

Computing FM and assesing if this provides significant difference to the results.

mathieuboudreau commented 1 week ago

Is the jaggedness at the edge of the lungs an image compression issue, or really what the segmentations are like now?

sriosq commented 1 week ago

The lungs look like this:

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I tried gaussian smoothign but it seems to not change. I don't want to over edit it I might change the segmentation drastically like before.

sriosq commented 1 week ago

@mathieuboudreau Update:

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Smoothing it outside segment and also the inside of the lungs, plus the skull and the trachea too!

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mathieuboudreau commented 1 week ago

Those look much better to me!