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Denoise kernel size #22

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mattcieslak opened this issue Jul 10, 2019 · 7 comments
Closed

Denoise kernel size #22

mattcieslak opened this issue Jul 10, 2019 · 7 comments
Labels
enhancement New feature or request GRE - phase1&2 GRE - phasediff SEI - Spiral Echo Imaging
Milestone
2.0.0

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@mattcieslak
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I'm finding for some older phase1/phase2 fieldmaps that it's necessary to set the kernel size to 5 for this node: https://github.com/poldracklab/sdcflows/blob/0.0.2/sdcflows/workflows/phdiff.py#L98

Is there a downside to setting the default to 5? Or should we make this a parameter?
@effigies
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Does it make sense to set a target smoothness instead of a straight kernel smoothing, as with 3dBlurToFWHM? Then we're less dependent on the quality of the input data.

@oesteban
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oesteban commented Aug 7, 2019

Hopefully, this will not be necessary after #14, but it doesn't hurt to first get this done.

@mattcieslak
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For now I have the kernel size only go up to 5 if there are two phase maps (#30) and the size stays 3 for phasediff images. #30 also re-organizes the workflows so that #14 can be used on these fieldmaps

oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 25, 2019
@oesteban
ENH: Base implementation for phase1/2 fieldmaps
1198fa5 
Putting together the lessons learned in nipreps#30, leveraging nipreps#52 and nipreps#53
(unfolded from nipreps#30 too), and utilizing nipreps#50 and nipreps#51, this workflow adds
the phase difference map calculation, considering it one use-case of the
general phase-difference fieldmap workflow.

On top of this PR, we can continue the discussions held in nipreps#30.
Probably, we will want to address nipreps#23 the first - the magnitude
segmentation is sometimes really bad (e.g. see the phase1/2 unit test).

Another discussion arisen in nipreps#30 is the spatial smoothing of the
fieldmap (nipreps#22).

Finally, the plan is to revise this implementation and determine whether
the subtraction should happen before or after PRELUDE, and whether the
arctan2 route is more interesting.
@oesteban oesteban mentioned this issue Nov 25, 2019
Merged
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 25, 2019
@oesteban
ENH: Base implementation for phase1/2 fieldmaps
bb08171 
Putting together the lessons learned in nipreps#30, leveraging nipreps#52 and nipreps#53
(unfolded from nipreps#30 too), and utilizing nipreps#50 and nipreps#51, this workflow adds
the phase difference map calculation, considering it one use-case of the
general phase-difference fieldmap workflow.

On top of this PR, we can continue the discussions held in nipreps#30.
Probably, we will want to address nipreps#23 the first - the magnitude
segmentation is sometimes really bad (e.g. see the phase1/2 unit test).

Another discussion arisen in nipreps#30 is the spatial smoothing of the
fieldmap (nipreps#22).

Finally, the plan is to revise this implementation and determine whether
the subtraction should happen before or after PRELUDE, and whether the
arctan2 route is more interesting.
@oesteban oesteban mentioned this issue Nov 25, 2019
Closed
@oesteban oesteban added this to the 1.1.0 milestone Nov 25, 2019
@oesteban
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I've set 5 as the default for now, and I'm pretty happy with the results.

I'm also with @effigies that 3dBlurToFWHM is a very cheap but effective solution to the problem.

Finally, we need to investigate the resampling when moving the fieldmap to the target EPI dataset because I'm under the impression that it is introducing some little spikes in it.

@mattcieslak
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Isn't 3dBlurToFWHM doing Gaussian smoothing instead of a median filter? I thought the main purpose was to remove spikes, which would end up getting spread out spatially if you just smooth with a Gaussian kernel.

@oesteban
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Isolated spikes would be removed with a Gaussian filter easily - median filters are better for salt&pepper kind of noise. It doesn't hurt to try.

But yes, you are right - the median filter is just to remove spikes

@oesteban oesteban modified the milestones: 1.2.0, 1.3.0 Dec 18, 2019
@oesteban oesteban mentioned this issue Apr 15, 2020
Closed
1 task
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 14, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
f11e35e 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: nipreps#71, nipreps#22.
Resolves: nipreps#72.
Resolves: nipreps#14.
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 14, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
eed5db6 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: nipreps#71, nipreps#22.
Resolves: nipreps#72.
Resolves: nipreps#14.
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 14, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
f1d4271 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: nipreps#71, nipreps#22.
Resolves: nipreps#72.
Resolves: nipreps#14.
@oesteban oesteban mentioned this issue Nov 14, 2020
Merged
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 14, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
c363a9d 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: nipreps#71, nipreps#22.
Resolves: nipreps#72.
Resolves: nipreps#14.
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 14, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
02a3b46 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: nipreps#71, nipreps#22.
Resolves: nipreps#72.
Resolves: nipreps#14.
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 16, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
a50b2c3 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: nipreps#71, nipreps#22.
Resolves: nipreps#72.
Resolves: nipreps#14.
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 16, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
3dd0aab 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: nipreps#71, nipreps#22.
Resolves: nipreps#72.
Resolves: nipreps#14.
@oesteban oesteban modified the milestones: 1.5.0, 1.4.0 Nov 18, 2020
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 19, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
00405f8 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: nipreps#71, nipreps#22.
Resolves: nipreps#72.
Resolves: nipreps#14.
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 22, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
8ad0e0e 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: nipreps#71, nipreps#22.
Resolves: nipreps#72.
Resolves: nipreps#14.
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 22, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
b615e3e 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: nipreps#71, nipreps#22.
Resolves: nipreps#72.
Resolves: nipreps#14.
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 25, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
7b2d602 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: nipreps#71, nipreps#22.
Resolves: nipreps#72.
Resolves: nipreps#14.
@oesteban
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Superseded by #119.

oesteban added a commit that referenced this issue Nov 26, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
339cd5a 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: #71, #22.
Resolves: #72.
Resolves: #14.
oesteban added a commit that referenced this issue Nov 30, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
7d3f10d 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: #71, #22.
Resolves: #72.
Resolves: #14.
oesteban added a commit that referenced this issue Dec 1, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
88cceab 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: #71, #22.
Resolves: #72.
Resolves: #14.
oesteban added a commit that referenced this issue Dec 3, 2020
@oesteban
ENH: A 3D tensor B-Spline approximator and extrapolator
74496c5 
This PR finally adds an implementation for B-Spline smoothing and
extrapolation of fieldmaps.

References: #71, #22.
Resolves: #72.
Resolves: #14.
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enhancement New feature or request GRE - phase1&2 GRE - phasediff SEI - Spiral Echo Imaging
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Milestone
2.0.0
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@effigies @mattcieslak @oesteban