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FSL-less version #1032

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araikes opened this issue Oct 7, 2022 · 2 comments · Fixed by #1108
Closed

FSL-less version #1032

araikes opened this issue Oct 7, 2022 · 2 comments · Fixed by #1108

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@araikes
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araikes commented Oct 7, 2022

HI @oesteban,

I love MRIQC but have a particular application for which an FSL-less version (or at least a version that gives an "no FSL" running option) would be invaluable. I know there had been some effort to move in that direction at one point and I'm just curious what the status might be.

Thanks
@oesteban
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The plan is clear, and the tooling around MRIQC seems going in the right direction (e.g., the recent addition of SynthStrip for brain extraction).

Are you most interested on anatomical images, BOLD, or both anatomical and functional?

@araikes
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araikes commented Oct 10, 2022

Ideally, we're looking for the ability to run both pipelines, however anatomical would be the priority.

@oesteban oesteban mentioned this issue Mar 10, 2023
Closed
oesteban added a commit that referenced this issue Mar 29, 2023
@oesteban
enh: replace FSL FAST with ANTs Atropos for brain tissue segmentation
4fc0ca9 
One more step toward #1032.

Partially-Supersedes: #803, #832.
@oesteban oesteban mentioned this issue Mar 29, 2023
Merged
oesteban added a commit that referenced this issue Mar 29, 2023
@oesteban
enh: replace FSL FAST with ANTs Atropos for brain tissue segmentation
8007e2a 
One more step toward #1032.

Partially-Supersedes: #803, #832.
oesteban added a commit that referenced this issue Mar 29, 2023
@oesteban
enh: replace FSL FAST with ANTs Atropos for brain tissue segmentation
8967c10 
One more step toward #1032.

Partially-Supersedes: #803, #832.
@oesteban oesteban mentioned this issue Mar 29, 2023
Closed
3 tasks
oesteban added a commit that referenced this issue Mar 30, 2023
@oesteban
enh: drop FSL BET to estimate the "outskin" (head) mask
7338217 
This PR contributes toward #1032 by eliminating the need for FSL BET.

By using an implementation closer to the gradient-based of (Mortamet,
2009), there is no more need for BET.
@oesteban oesteban mentioned this issue Mar 30, 2023
Merged
oesteban added a commit that referenced this issue Apr 1, 2023
@oesteban
enh: replace FSL FAST with ANTs Atropos for brain tissue segmentation
987f1ef 
One more step toward #1032.

Partially-Supersedes: #803, #832.
oesteban added a commit that referenced this issue Apr 1, 2023
@oesteban
enh: replace FSL FAST with ANTs Atropos for brain tissue segmentation
8589e33 
One more step toward #1032.

Partially-Supersedes: #803, #832.
oesteban added a commit that referenced this issue Apr 3, 2023
@oesteban
enh: drop FSL MELODIC (without alternative)
d9f992d 
After careful consideration, I'm proposing to drop the ``--ica``
argument of the functional workflow, to continue toward eliminating
FSL as a dependency.

The reason is that the ICA decomposition does not seem (alone)
sufficient to assess the quality.
Or at least, the kind of problems/artifacts you can pick with just the
ICA decomposition (without assistance like CompCor, AROMA or FIX) are
typically identifiable with the standard deviation image and other
mosaics.

I would not be against adding sklearn's FastICA or a reimplementation
of MELODIC to have the ICA + EM mixtrue modelling, but, for now, I
believe the priority should be to finally remove FSL, even if that means
discontinuing a feature.

Other than the visual reports, there's no other side effect since we are
currently not calculating any IQMs from the ICA results (which would be
a very interesting addition in the future, perhaps with some AROMA
assistance).

Relates: #1032.
@oesteban oesteban mentioned this issue Apr 3, 2023
Merged
oesteban added a commit that referenced this issue Apr 3, 2023
@oesteban
enh: replace FSL FAST with ANTs Atropos for brain tissue segmentation
19510c4 
One more step toward #1032.

Partially-Supersedes: #803, #832.
oesteban added a commit that referenced this issue Apr 4, 2023
@oesteban
enh: replace FSL FAST with ANTs Atropos for brain tissue segmentation
50b3109 
One more step toward #1032.

Partially-Supersedes: #803, #832.
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ENH: Culminate dropping FSL as a dependency nipreps/mriqc
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@oesteban @araikes