Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

FIX: Refactoring the B0FieldTransform implementation #346

Merged
merged 44 commits into from
Aug 16, 2023
Merged

FIX: Refactoring the B0FieldTransform implementation #346

Show file tree
Hide file tree
Changes from 39 commits
Commits
Show all changes
44 commits
Select commit Hold shift + click to select a range
6380300
fix: refactoring the ``B0FieldTransform`` implementation
oesteban Apr 7, 2023
c23e4f1
enh: draft the approx branch
oesteban Apr 7, 2023
0e2970d
Update sdcflows/transform.py
oesteban Apr 18, 2023
eb10851
enh: incorporate dense resampling of fieldmap
oesteban Apr 27, 2023
855d4cd
sty: add typing annotations and run black
oesteban May 2, 2023
c4b25f4
fix: miscellaneous problems
oesteban May 2, 2023
dcb640d
fix: do not accept multiple files
oesteban May 2, 2023
6de06d7
fix: parallelize resampling of 4D images
oesteban Jun 30, 2023
d1a69c3
ref: cleanup code in preparation of head motion
oesteban Jun 30, 2023
37ded68
feat: defer head-motion correction into parallel unwarp
oesteban Jun 30, 2023
9757cff
fix: interface internal streamlining toward getting tests to pass
oesteban Jun 30, 2023
8838140
Update sdcflows/transform.py
oesteban Jul 2, 2023
f07b4d0
Update sdcflows/transform.py
oesteban Jul 2, 2023
489b135
Update sdcflows/transform.py
oesteban Jul 2, 2023
54ea466
fix: resolve undefined variable
oesteban Jul 2, 2023
a86fd3e
fix/doc: revise docstrings, remove cache validation
oesteban Jul 3, 2023
37a8b0d
doc: fix documentation and cross-references
oesteban Jul 3, 2023
303b5ee
fix: adapt test with new API of the ApplyCoeffsField interface
oesteban Jul 3, 2023
7f4a2ae
fix: roll back interface to allow varying pe_dirs/ro_times within a s…
oesteban Jul 4, 2023
9a52a82
fix: ensure positive cosines seems necessary before fitting
oesteban Jul 4, 2023
e3129ca
fix: connections in debug version of pipeline
oesteban Jul 4, 2023
cbac298
Apply suggestions from code review
oesteban Jul 6, 2023
7027b23
fix: test on more frequentist terms
oesteban Jul 4, 2023
80b4449
fix: add connection to feed fmap2data transform
oesteban Jul 6, 2023
d1c696a
maint: add test of fit-pepolar/apply workflows
oesteban Jul 7, 2023
f2fe091
fix: revise type of input to bspline interface
oesteban Jul 7, 2023
03273dd
fix: error in test because of connection removed
oesteban Jul 7, 2023
9cbc0ab
maint: add unittest on B0FieldTransform with hcph data
oesteban Jul 7, 2023
5c0ab56
fix/feat: add GRE fieldmaps of hcph to integration tests (fix applyco…
oesteban Jul 7, 2023
7825b28
sty: run black on changed files
oesteban Jul 7, 2023
eebd043
fix(wip): forward the fmap2epi transform
oesteban Jul 7, 2023
dc5bfae
Remove pdb trace
effigies Jul 7, 2023
fe39d0d
fix: apply cannot be done on np.ndarray
oesteban Jul 10, 2023
9fef23d
maint: update nitransforms pin
oesteban Jul 10, 2023
2b1fc96
enh: do not approx if coefficients and target grid are aligned
oesteban Jul 12, 2023
f223ae1
maint: add PA/AP tests with one more session of data
oesteban Jul 12, 2023
ab21381
fix: revise registration workflow
oesteban Aug 7, 2023
01ef011
enh: add parameterized test on the transform
oesteban Aug 8, 2023
53663d4
fix+enh: wrong transform creating NIfTI object + move to transform po…
oesteban Aug 8, 2023
0f24b6b
enh: disable head-motion transforms consideration
oesteban Aug 11, 2023
2e72608
Apply suggestions from code review
oesteban Aug 16, 2023
107f56e
fix+sty: argument specification + run black
oesteban Aug 16, 2023
ea12e7f
Apply suggestions from code review
oesteban Aug 16, 2023
6e3de3a
enh: address comments from code review
oesteban Aug 16, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 7 additions & 0 deletions .circleci/config.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,13 @@ jobs:
datalad install -r https://gin.g-node.org/nipreps-data/brain-extraction-tests
datalad update --merge -d brain-extraction-tests/
datalad get -r -J 2 -d brain-extraction-tests

- run:
name: Install HCPh fieldmaps
command: |
datalad install -r https://github.com/nipreps-data/hcph-pilot_fieldmaps.git
datalad update -r --merge -d hcph-pilot_fieldmaps/
datalad get -r -J 2 -d hcph-pilot_fieldmaps/ hcph-pilot_fieldmaps/*

- save_cache:
key: data-v6-{{ .Branch }}-{{ .Revision }}
Expand Down
3 changes: 2 additions & 1 deletion sdcflows/data/fmap-any_registration.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,5 +18,6 @@
"transforms": [ "Rigid", "Rigid" ],
"use_histogram_matching": [ true, true ],
"winsorize_lower_quantile": 0.001,
"winsorize_upper_quantile": 0.999
"winsorize_upper_quantile": 0.999,
"write_composite_transform": false
}
3 changes: 2 additions & 1 deletion sdcflows/data/fmap-any_registration_testing.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,5 +18,6 @@
"transforms": [ "Rigid", "Rigid" ],
"use_histogram_matching": [ true, true ],
"winsorize_lower_quantile": 0.005,
"winsorize_upper_quantile": 0.998
"winsorize_upper_quantile": 0.998,
"write_composite_transform": false
}
Loading