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Merge pull request #439 from bids-standard/bfm
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[FIX] fix spelling and set up codespell
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@Remi-Gau
Remi-Gau authored Apr 20, 2024
2 parents f60cd97 + 7557f2e commit 9a4cc30
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4 changes: 4 additions & 0 deletions .codespellrc
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[codespell]
skip = .git,env,venv,ds*,asl*,qmr*,genetics*,fnirs*,eeg*,meg*,pet*,ieeg*,motion*,synthetic*
builtin = clear,rare
ignore-words-list = nd
20 changes: 20 additions & 0 deletions .github/workflows/validation.yml
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---
name: Validation

on:
push:
branches: [master]
pull_request:
branches: [master]

concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true

jobs:
# Check for common misspellings
codespell:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: codespell-project/actions-codespell@master
16 changes: 8 additions & 8 deletions README.md
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Expand Up @@ -132,7 +132,7 @@ DO NOT EDIT DIRECTLY.
| [asl001](https://github.com/bids-standard/bids-examples/tree/master/asl001) | T1w, asl (GE, PCASL, 3D_SPIRAL), m0scan within timeseries | anat, perf | T1w, asl, aslcontext, asllabeling | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) |
| [asl002](https://github.com/bids-standard/bids-examples/tree/master/asl002) | T1w, asl (Philips, PCASL, 2D_EPI), m0scan as separate scan | anat, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) |
| [asl003](https://github.com/bids-standard/bids-examples/tree/master/asl003) | T1w, asl (Siemens, PASL, multiTI), M0scan as separate scan | anat, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) |
| [asl004](https://github.com/bids-standard/bids-examples/tree/master/asl004) | T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar appraoch | anat, fmap, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) |
| [asl004](https://github.com/bids-standard/bids-examples/tree/master/asl004) | T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar approach | anat, fmap, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) |
| [asl005](https://github.com/bids-standard/bids-examples/tree/master/asl005) | T1w, asl (Siemens, PCASL, singleTI, 3D_GRASE), m0scan as separate scan | anat, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) |

### EEG
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| name | description | datatypes | suffixes | link to full data | maintained by |
|:--------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------|:------------|:-------------------------------------------------------|:------------------------------|:-------------------------------------------------------------|
| [qmri_irt1](https://github.com/bids-standard/bids-examples/tree/master/qmri_irt1) | Inversion Recovery T1 mapping | anat | IRT1 | `not publicly availabe` | [@agahkarakuzu](https://github.com/agahkarakuzu) |
| [qmri_megre](https://github.com/bids-standard/bids-examples/tree/master/qmri_megre) | Multi-Echo Gradient-Echo for T2star mapping. | anat | MEGRE | `not publicly availabe` | [@agahkarakuzu](https://github.com/agahkarakuzu) |
| [qmri_mese](https://github.com/bids-standard/bids-examples/tree/master/qmri_mese) | Multi-Echo Spin-Echo for T2 or Myelin Water Fraction (MWF) mapping. | anat | MESE | `not publicly availabe` | [@agahkarakuzu](https://github.com/agahkarakuzu) |
| [qmri_irt1](https://github.com/bids-standard/bids-examples/tree/master/qmri_irt1) | Inversion Recovery T1 mapping | anat | IRT1 | `not publicly available` | [@agahkarakuzu](https://github.com/agahkarakuzu) |
| [qmri_megre](https://github.com/bids-standard/bids-examples/tree/master/qmri_megre) | Multi-Echo Gradient-Echo for T2star mapping. | anat | MEGRE | `not publicly available` | [@agahkarakuzu](https://github.com/agahkarakuzu) |
| [qmri_mese](https://github.com/bids-standard/bids-examples/tree/master/qmri_mese) | Multi-Echo Spin-Echo for T2 or Myelin Water Fraction (MWF) mapping. | anat | MESE | `not publicly available` | [@agahkarakuzu](https://github.com/agahkarakuzu) |
| [qmri_mp2rage](https://github.com/bids-standard/bids-examples/tree/master/qmri_mp2rage) | MP2RAGE for T1 mapping | anat | MP2RAGE, defacemask | [link](https://osf.io/k4bs5/) | [@Gilles86](https://github.com/Gilles86) |
| [qmri_mp2rageme](https://github.com/bids-standard/bids-examples/tree/master/qmri_mp2rageme) | Multi-echo MP2RAGE | anat, fmap | MP2RAGE, TB1map | [link](https://osf.io/k4bs5/) | [@Gilles86](https://github.com/Gilles86) |
| [qmri_mpm](https://github.com/bids-standard/bids-examples/tree/master/qmri_mpm) | Multi-parametric mapping for R1, R2star, MTsat and PD mapping | anat, fmap | MPM, RB1COR, TB1EPI, magnitude1, magnitude2, phasediff | [link](https://osf.io/k4bs5/) | [@ChristophePhillips](https://github.com/ChristophePhillips) |
| [qmri_mtsat](https://github.com/bids-standard/bids-examples/tree/master/qmri_mtsat) | Example dataset for T1 and MTsat mapping. Includes a double-angle B1+ mapping example. | anat, fmap | MTS, TB1DAM | [link](https://osf.io/k4bs5/) | [@agahkarakuzu](https://github.com/agahkarakuzu) |
| [qmri_qsm](https://github.com/bids-standard/bids-examples/tree/master/qmri_qsm) | Chimap using fast QSM | anat | T1w | `not publicly availabe` | [@agahkarakuzu](https://github.com/agahkarakuzu) |
| [qmri_sa2rage](https://github.com/bids-standard/bids-examples/tree/master/qmri_sa2rage) | Fast B1+ mapping using SA2RAGE | fmap | TB1SRGE | `not publicly availabe` | [@agahkarakuzu](https://github.com/agahkarakuzu) |
| [qmri_tb1tfl](https://github.com/bids-standard/bids-examples/tree/master/qmri_tb1tfl) | B1+ mapping with TurboFLASH readout. | fmap | TB1TFL | `not publicly availabe` | [@agahkarakuzu](https://github.com/agahkarakuzu) |
| [qmri_qsm](https://github.com/bids-standard/bids-examples/tree/master/qmri_qsm) | Chimap using fast QSM | anat | T1w | `not publicly available` | [@agahkarakuzu](https://github.com/agahkarakuzu) |
| [qmri_sa2rage](https://github.com/bids-standard/bids-examples/tree/master/qmri_sa2rage) | Fast B1+ mapping using SA2RAGE | fmap | TB1SRGE | `not publicly available` | [@agahkarakuzu](https://github.com/agahkarakuzu) |
| [qmri_tb1tfl](https://github.com/bids-standard/bids-examples/tree/master/qmri_tb1tfl) | B1+ mapping with TurboFLASH readout. | fmap | TB1TFL | `not publicly available` | [@agahkarakuzu](https://github.com/agahkarakuzu) |
| [qmri_vfa](https://github.com/bids-standard/bids-examples/tree/master/qmri_vfa) | Variable Flip Angle T1 mapping. Includes an Actual Flip Angle (AFI) B1+ mapping example. | anat, fmap | TB1AFI, VFA | [link](https://osf.io/k4bs5/) | [@agahkarakuzu](https://github.com/agahkarakuzu) |

### Behavioral
Expand All @@ -304,4 +304,4 @@ DO NOT EDIT DIRECTLY.
|:------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------------------------|:-------------------------------------------------------------------------------------------------------------|:-------------------------------------------------|:-------------------------------------------|
| [ds000117](https://github.com/bids-standard/bids-examples/tree/master/ds000117) | A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task | anat, beh, dwi, fmap, func, meg | T1w, beh, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) |
| [eeg_ds003645s_hed_demo](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_demo) | Shows usage of Hierarchical Event Descriptor (HED) in .tsv files | eeg, beh | channels, eeg, events, participants, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) |
| [synthetic](https://github.com/bids-standard/bids-examples/tree/master/synthetic) | A synthetic dataset | anat, beh, func | T1w, beh, bold, events, physio, scans, sessions, stim | n/a | [@effigies](https://github.com/effigies) |
| [synthetic](https://github.com/bids-standard/bids-examples/tree/master/synthetic) | A synthetic dataset | anat, beh, func | T1w, beh, bold, events, physio, scans, sessions, stim | n/a | [@effigies](https://github.com/effigies) |
14 changes: 7 additions & 7 deletions dataset_listing.tsv
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Expand Up @@ -38,19 +38,19 @@ ds004332 Anat dataset with task entity [link](https://openneuro.org/datasets/ds0
asl001 T1w, asl (GE, PCASL, 3D_SPIRAL), m0scan within timeseries [link](https://osf.io/yru2q/) [@patsycle](https://github.com/patsycle) anat, perf T1w, asl, aslcontext, asllabeling
asl002 T1w, asl (Philips, PCASL, 2D_EPI), m0scan as separate scan [link](https://osf.io/yru2q/) [@patsycle](https://github.com/patsycle) anat, perf T1w, asl, aslcontext, asllabeling, m0scan
asl003 T1w, asl (Siemens, PASL, multiTI), M0scan as separate scan [link](https://osf.io/yru2q/) [@patsycle](https://github.com/patsycle) anat, perf T1w, asl, aslcontext, asllabeling, m0scan
asl004 T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar appraoch [link](https://osf.io/yru2q/) [@patsycle](https://github.com/patsycle) anat, fmap, perf T1w, asl, aslcontext, asllabeling, m0scan
asl004 T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar approach [link](https://osf.io/yru2q/) [@patsycle](https://github.com/patsycle) anat, fmap, perf T1w, asl, aslcontext, asllabeling, m0scan
asl005 T1w, asl (Siemens, PCASL, singleTI, 3D_GRASE), m0scan as separate scan [link](https://osf.io/yru2q/) [@patsycle](https://github.com/patsycle) anat, perf T1w, asl, aslcontext, asllabeling, m0scan
qmri_mp2rage MP2RAGE for T1 mapping [link](https://osf.io/k4bs5/) [@Gilles86](https://github.com/Gilles86) anat MP2RAGE, defacemask
qmri_mp2rageme Multi-echo MP2RAGE [link](https://osf.io/k4bs5/) [@Gilles86](https://github.com/Gilles86) anat, fmap MP2RAGE, TB1map
qmri_mpm Multi-parametric mapping for R1, R2star, MTsat and PD mapping [link](https://osf.io/k4bs5/) [@ChristophePhillips](https://github.com/ChristophePhillips) anat, fmap MPM, RB1COR, TB1EPI, magnitude1, magnitude2, phasediff
qmri_mtsat Example dataset for T1 and MTsat mapping. Includes a double-angle B1+ mapping example. [link](https://osf.io/k4bs5/) [@agahkarakuzu](https://github.com/agahkarakuzu) anat, fmap MTS, TB1DAM
qmri_qsm Chimap using fast QSM `not publicly availabe` [@agahkarakuzu](https://github.com/agahkarakuzu) anat T1w
qmri_sa2rage Fast B1+ mapping using SA2RAGE `not publicly availabe` [@agahkarakuzu](https://github.com/agahkarakuzu) fmap TB1SRGE
qmri_qsm Chimap using fast QSM `not publicly available` [@agahkarakuzu](https://github.com/agahkarakuzu) anat T1w
qmri_sa2rage Fast B1+ mapping using SA2RAGE `not publicly available` [@agahkarakuzu](https://github.com/agahkarakuzu) fmap TB1SRGE
qmri_vfa Variable Flip Angle T1 mapping. Includes an Actual Flip Angle (AFI) B1+ mapping example. [link](https://osf.io/k4bs5/) [@agahkarakuzu](https://github.com/agahkarakuzu) anat, fmap TB1AFI, VFA
qmri_irt1 Inversion Recovery T1 mapping `not publicly availabe` [@agahkarakuzu](https://github.com/agahkarakuzu) anat IRT1
qmri_mese Multi-Echo Spin-Echo for T2 or Myelin Water Fraction (MWF) mapping. `not publicly availabe` [@agahkarakuzu](https://github.com/agahkarakuzu) anat MESE
qmri_megre Multi-Echo Gradient-Echo for T2star mapping. `not publicly availabe` [@agahkarakuzu](https://github.com/agahkarakuzu) anat MEGRE
qmri_tb1tfl B1+ mapping with TurboFLASH readout. `not publicly availabe` [@agahkarakuzu](https://github.com/agahkarakuzu) fmap TB1TFL
qmri_irt1 Inversion Recovery T1 mapping `not publicly available` [@agahkarakuzu](https://github.com/agahkarakuzu) anat IRT1
qmri_mese Multi-Echo Spin-Echo for T2 or Myelin Water Fraction (MWF) mapping. `not publicly available` [@agahkarakuzu](https://github.com/agahkarakuzu) anat MESE
qmri_megre Multi-Echo Gradient-Echo for T2star mapping. `not publicly available` [@agahkarakuzu](https://github.com/agahkarakuzu) anat MEGRE
qmri_tb1tfl B1+ mapping with TurboFLASH readout. `not publicly available` [@agahkarakuzu](https://github.com/agahkarakuzu) fmap TB1TFL
pet001 T1w, PET, blood [@mnoergaard](https://github.com/mnoergaard) anat, pet T1w, blood, pet
pet002 T1w, PET [link](https://openneuro.org/datasets/ds001420/) [@mnoergaard](https://github.com/mnoergaard) anat, pet T1w, pet
pet003 T1w, PET, blood [@mnoergaard](https://github.com/mnoergaard) anat, pet T1w, blood, pet
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