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Python code for flexible pipeline control
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pydpiper 2.0.5 MBM nlin_mask maybe should be voxel_voted? #315

Open gdevenyi opened 7 years ago

gdevenyi commented 7 years ago

Rather than "-max"ing the candidate masks, perhaps voxel_voting the mask would result in a tighter mask while still being accurate?

bcdarwin commented 7 years ago

It's funny you would say this ... in the maget_mask function we do voxel_vote the masks and we're thinking of switching to max, because this sometimes cuts off some voxels of the brain. This might indeed work better after a mincANTS nonlinear registration than in maget_mask, though.

From: Gabriel A. Devenyi [notifications@github.com] Sent: January 24, 2017 2:42 PM To: Mouse-Imaging-Centre/pydpiper Cc: Subscribed Subject: [Mouse-Imaging-Centre/pydpiper] pydpiper 2.0.5 MBM nlin_mask maybe should be voxel_voted? (#315)

Rather than "-max"ing the candidate masks, perhaps voxel_voting the mask would result in a tighter mask while still being accurate?

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gdevenyi commented 6 years ago

So, I have a strong argument against -max.

We just had one subject go off the rails in twolevel. Since twolevel masking is subject specific MAGeT's voting didn't save us. Its masking error propagated to the final mask because of "-max"

gdevenyi commented 6 years ago

Maybe dilate the final mask after voxel vote to include the missing voxels?

bcdarwin commented 6 years ago

I've also had this happen recently. We could add dilation of a configurable number of voxels (or whatever) and possibly also some voting threshold so you could interpolate between majority vote and 'max'.

From: Gabriel A. Devenyi notifications@github.com Sent: November 23, 2017 4:19:29 PM To: Mouse-Imaging-Centre/pydpiper Cc: Benjamin Darwin; Comment Subject: Re: [Mouse-Imaging-Centre/pydpiper] pydpiper 2.0.5 MBM nlin_mask maybe should be voxel_voted? (#315)

Maybe dilate the final mask after voxel vote to include the missing voxels?

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gdevenyi commented 5 years ago

Just following up on my various issues, I totally agree with the choice to "-max" vote the maget masks. An under segmentation at that stage propagates down through the model build in a bad way.