ENH: Replace initial FLIRT with mri_coreg, use -basescale 1 for FLIRT-BBR

[effigies]

Rebases #2607 on master.

Fast-tracked to get this into the next 21.0.0 RC. Need to figure out numpy failures in the docker image to patch 20.2.x.

[effigies]

@mgxd We need to update the reports and boilerplate to indicate that we're using mri_coreg. Not sure it's worth doing before an RC. Let me know if I should work on this or start a new PR.

[mgxd]

Once we get niworkflows passing, I'll kick off the release chain, but I don't expect we'll get to fmriprep until Monday. Depending on how long you think those updates will take, you can probably just do it here.

[effigies]

Ah, niworkflows is going to be at least two hours to finish the mask regression tests. I'll see what I can get to by 5.

[effigies]

Not really sure how to fix this in the citation boilerplate (from artifacts:

Functional data preprocessing

: For each of the 1 BOLD runs found per subject (across all
tasks and sessions), the following preprocessing was performed.

Preprocessing of B0 inhomogeneity mappings

: A total of 1 fieldmaps were found available within the input
BIDS structure for this particular subject.
A deformation field to correct for susceptibility distortions was estimated
based on *fMRIPrep*'s *fieldmap-less* approach.
The deformation field is that resulting from co-registering the EPI reference
to the same-subject T1w-reference with its intensity inverted [@fieldmapless1;
@fieldmapless2].
Registration is performed with `antsRegistration`
(ANTs 2.3.3), and
the process regularized by constraining deformation to be nonzero only
along the phase-encoding direction, and modulated with an average fieldmap
template [@fieldmapless3].
First, a reference volume and its skull-stripped version were generated
from the shortest echo of the BOLD run using a custom
methodology of *fMRIPrep*.
[...]

Pretty sure it should be

Preprocessing of B0 inhomogeneity mappings

: A total of 1 fieldmaps were found available within the input
BIDS structure for this particular subject.
A deformation field to correct for susceptibility distortions was estimated
based on *fMRIPrep*'s *fieldmap-less* approach.
The deformation field is that resulting from co-registering the EPI reference
to the same-subject T1w-reference with its intensity inverted [@fieldmapless1;
@fieldmapless2].
Registration is performed with `antsRegistration`
(ANTs 2.3.3), and
the process regularized by constraining deformation to be nonzero only
along the phase-encoding direction, and modulated with an average fieldmap
template [@fieldmapless3].

Functional data preprocessing

: For each of the 1 BOLD runs found per subject (across all
tasks and sessions), the following preprocessing was performed.
First, a reference volume and its skull-stripped version were generated
from the shortest echo of the BOLD run using a custom
methodology of *fMRIPrep*.
[...]

[codecov-commenter]

Codecov Report

Merging #2625 (c52206f) into master (d2ad203) will decrease coverage by 0.02%.
The diff coverage is 20.00%.

@@            Coverage Diff             @@
##           master    #2625      +/-   ##
==========================================
- Coverage   45.46%   45.43%   -0.03%     
==========================================
  Files          41       41              
  Lines        3161     3163       +2     
==========================================
  Hits         1437     1437              
- Misses       1724     1726       +2     

Impacted Files	Coverage Δ
fmriprep/workflows/bold/registration.py	8.88% <20.00%> (-0.10%)	⬇️

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[effigies]

@oesteban As the master of the literate workflows, your advice on how to rearrange the boilerplate text would be appreciated.

[mgxd]

I was looking into this earlier - from my understanding, order largely depends on the graph order, though __predesc__, __desc__, and __postdesc__ can somewhat help. LiterateWorkflow likely needs a change to allow more fine control within these sections.

[oesteban]

@oesteban As the master of the literate workflows, your advice on how to rearrange the boilerplate text would be appreciated.

I'm not sure this problem has been introduced here - we probably should get this merged and keep investigating why the boilerplate is garbled.

order largely depends on the graph order, though __predesc__, __desc__, and __postdesc__ can somewhat help. LiterateWorkflow likely needs a change to allow more fine control within these sections.

Agreed.

[effigies]

No it wasn't introduced here. Was just interested in fixing it. I'm okay with merging this as is.