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[ENH] Allow .bval and .bvec files for pepolar fmaps #1754

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merged 17 commits into from
Apr 24, 2024
Merged

[ENH] Allow .bval and .bvec files for pepolar fmaps #1754

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4e1c118
add epi.bval, epi.bvec
mattcieslak Mar 29, 2024
c70cc60
update contributors.md
mattcieslak Mar 29, 2024
72fb130
add lines for sentence
mattcieslak Mar 29, 2024
f9ffc23
update preprocessed_data.yaml
mattcieslak Mar 29, 2024
79689b1
override for m0scan
mattcieslak Mar 29, 2024
b12405d
Update src/schema/rules/files/deriv/preprocessed_data.yaml
mattcieslak Mar 29, 2024
47c7ff3
Whitespace and table pipes
mattcieslak Mar 29, 2024
da2ff54
remove ref
mattcieslak Mar 29, 2024
cfd1101
Add EPI-with-b[val|vec] suffix checks.
tsalo Apr 4, 2024
7370a63
Merge branch 'master' into add_epi_bval_bvec
tsalo Apr 4, 2024
b6ec4dc
Merge remote-tracking branch 'upstream/master' into add_epi_bval_bvec
tsalo Apr 24, 2024
5801f2f
Add EPI+bval check.
tsalo Apr 24, 2024
389ab29
Remove Latin phrase.
tsalo Apr 24, 2024
abd2a5b
Update src/schema/rules/checks/fmap.yaml
tsalo Apr 24, 2024
aa954f0
Change max to min.
tsalo Apr 24, 2024
0cf5c0a
Address review.
tsalo Apr 24, 2024
7e5eae9
Bump schema version.
tsalo Apr 24, 2024
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1 change: 1 addition & 0 deletions src/appendices/contributors.md
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Expand Up @@ -257,6 +257,7 @@ If you contributed to the BIDS ecosystem and your name is not listed, please add
| Mateusz Pawlik | 📖🐛🤔🚧👀 |
| Mathias Goncalves | 💻🔧📢 |
| Mathieu Boudreau | 💬🤔📢 |
| Matt Cieslak | 📖 |
| Matt Sanderson | 📖💻 |
| Matteo Tonietto | 📖 |
| Matthias Günther | 📖 |
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3 changes: 2 additions & 1 deletion src/modality-specific-files/magnetic-resonance-imaging-data.md
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Expand Up @@ -1253,7 +1253,8 @@ The phase-encoding polarity (PEpolar) technique combines two or more Spin Echo
EPI scans with different phase encoding directions to estimate the distortion
map corresponding to the nonuniformities of the *B<sub>0</sub>* field.
These `*_epi.nii[.gz]` - or `*_m0scan.nii[.gz]` for arterial spin labeling perfusion data - files can be 3D or 4D --
in the latter case, all timepoints share the same scanning parameters.
in the latter case, all timepoints share the same scanning parameters. Some 4D scans intended
for correcting DWIs may have accompanying `*_epi.bval` and `*_epi.bvec` files.
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Examples of software tools using these kinds of images are FSL TOPUP and
AFNI `3dqwarp`.

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12 changes: 11 additions & 1 deletion src/schema/rules/files/raw/fmap.yaml
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Expand Up @@ -24,7 +24,6 @@ fieldmaps:
pepolar:
suffixes:
- epi
- m0scan
extensions:
- .nii.gz
- .nii
Expand All @@ -41,6 +40,17 @@ pepolar:
part: optional
chunk: optional

pepolar_m0scan:
$ref: rules.files.raw.fmap.pepolar
suffixes:
- m0scan

pepolar_dwi:
$ref: rules.files.raw.fmap.pepolar
extensions:
- .bval
- .bvec

TB1DAM:
suffixes:
- TB1DAM
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