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Remove QSIPrep-specific parameters and Config elements #6

Merged
merged 31 commits into from
Aug 13, 2024
Merged

Remove QSIPrep-specific parameters and Config elements #6

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890ed8e
Remove QSIPrep-specific parameters.
tsalo Aug 9, 2024
b221347
Drop QSIPrep-specific config elements.
tsalo Aug 9, 2024
231b36c
Update parser.py
tsalo Aug 9, 2024
2c87640
Merge branch 'main' into drop-prep-arguments
tsalo Aug 12, 2024
7539e8e
Replace qsirecon_dir with output_dir.
tsalo Aug 12, 2024
491c5a8
Update some stuff.
tsalo Aug 12, 2024
19941f4
Merge branch 'main' into drop-prep-arguments
tsalo Aug 12, 2024
683fd5b
Update usage.rst
tsalo Aug 12, 2024
539c3d5
Update usage.rst
tsalo Aug 12, 2024
ce0d606
Merge branch 'main' into drop-prep-arguments
tsalo Aug 12, 2024
438987c
Update.
tsalo Aug 12, 2024
605e046
Merge branch 'main' into drop-prep-arguments
tsalo Aug 12, 2024
78b2909
Update test_cli.py
tsalo Aug 12, 2024
bd2f337
Add `--b0-threshold` and `--skip-odf-reports` back.
tsalo Aug 12, 2024
67e72ad
Update test_cli.py
tsalo Aug 13, 2024
b4a8011
Drop skip_bids_validation.
tsalo Aug 13, 2024
f147fb4
Update opts_tests.py
tsalo Aug 13, 2024
6fe0d66
Update parser.py
tsalo Aug 13, 2024
e92f933
Update config.py
tsalo Aug 13, 2024
7467c42
Try this.
tsalo Aug 13, 2024
c122338
Update base.py
tsalo Aug 13, 2024
1a8a280
Try fixing.
tsalo Aug 13, 2024
b0371c8
Fix?
tsalo Aug 13, 2024
74fe339
Add output_resolution back in.
tsalo Aug 13, 2024
2ae80ca
More fix.
tsalo Aug 13, 2024
1a05eaa
Update mrtrix.py
tsalo Aug 13, 2024
66063d6
Update run.py
tsalo Aug 13, 2024
3b73ad5
Update run.py
tsalo Aug 13, 2024
b13b6b3
update tests
mattcieslak Aug 13, 2024
ef0d11d
update expected outputs
mattcieslak Aug 13, 2024
ae1457b
one more round
mattcieslak Aug 13, 2024
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64 changes: 0 additions & 64 deletions .circleci/AllFieldmaps.sh
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43 changes: 0 additions & 43 deletions .circleci/DRBUDDI_SHORELine_epi.sh
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40 changes: 0 additions & 40 deletions .circleci/DRBUDDI_TENSORLine_epi.sh
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43 changes: 0 additions & 43 deletions .circleci/DRBUDDI_eddy_rpe_series.sh
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51 changes: 0 additions & 51 deletions .circleci/DSCSDSI.sh
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48 changes: 0 additions & 48 deletions .circleci/DSCSDSI_outputs.txt
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49 changes: 0 additions & 49 deletions .circleci/DSDTI_TOPUP.sh
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49 changes: 0 additions & 49 deletions .circleci/DSDTI_nofmap.sh
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