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Support for optional intensity modulation in B0FieldTransform.apply() #238

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oesteban opened this issue Oct 1, 2021 · 0 comments
Open

Support for optional intensity modulation in B0FieldTransform.apply() #238

oesteban opened this issue Oct 1, 2021 · 0 comments
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effort: medium Estimated medium effort task impact: high Estimated high impact task unwarping
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20.0.13

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oesteban commented Oct 1, 2021

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@oesteban oesteban added unwarping impact: high Estimated high impact task effort: medium Estimated medium effort task labels Oct 1, 2021
@oesteban oesteban added this to the 2.0.8 milestone Oct 1, 2021
@oesteban oesteban self-assigned this Oct 1, 2021
oesteban added a commit to nipreps/fmriprep that referenced this issue Oct 20, 2021
@oesteban
fix: ME | Revise SDC compute graph
0ad307b 
Although I brought up the issue within #2530 and got some mildly opposed initial
opinion from @effigies
(#2530 (comment)),
I've come to think that we should provide the T2star workflow with
HMC'ed and SDC'ed echos (confirmation awaiting:
#2608 (review)).

This comes as an issue related to #2606.

This PR proposes that individual echoes are HMC'ed (and SDC'ed when
fieldmaps are available) before calculating the optimal combination
and the T2star map.

I believe this may be beneficial when we combine SDC with modulation by
the Jacobian of the distortion (nipreps/sdcflows#238) because that might
help restore some (little, admittedly) of the dropout of the later
echoes in distorted regions. I would expect more voxels will be deemed
as acceptable for the exponential fitting for this reason.

It also conceptually simplifies a little, as both SE and ME paths look
more alike, and only the little hacks to generate ME iterables and the
``boldbuffer`` are now necessary. Otherwise, SDC would be inserted at a
much later stage for ME only.
@oesteban oesteban mentioned this issue Oct 20, 2021
Merged
@oesteban oesteban modified the milestones: 2.0.8, 2.0.10 Nov 24, 2021
@effigies effigies modified the milestones: 2.0.10, 20.0.13 Feb 14, 2022
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