From afc340f4fc01e8564f6d84cdb4c54ff7d90d1540 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 10 Nov 2024 14:13:48 +0100 Subject: [PATCH 1/7] [ENH] move bids examples to a new page (#507) Co-authored-by: Chris Markiewicz --- .remarkignore | 2 +- data/datasets/examples | 2 +- docs/datasets/examples.md | 246 ++++++++++++++++++++++++++++++++++++++ docs/datasets/index.md | 202 ------------------------------- makefile | 2 +- mkdocs.yml | 1 + specification | 2 +- 7 files changed, 251 insertions(+), 206 deletions(-) create mode 100644 docs/datasets/examples.md diff --git a/.remarkignore b/.remarkignore index dd3b8306..4f78c206 100644 --- a/.remarkignore +++ b/.remarkignore @@ -1,3 +1,3 @@ docs/collaboration/bids_github/ -docs/datasets/index.md +docs/datasets/examples.md docs/extensions/macros_doc.md diff --git a/data/datasets/examples b/data/datasets/examples index fc84fd0f..2f634a14 160000 --- a/data/datasets/examples +++ b/data/datasets/examples @@ -1 +1 @@ -Subproject commit fc84fd0f42560973b605ce812c7cf490800449e5 +Subproject commit 2f634a14681587408a7c00f7dfbf6b22dba1e327 diff --git a/docs/datasets/examples.md b/docs/datasets/examples.md new file mode 100644 index 00000000..36edfcb0 --- /dev/null +++ b/docs/datasets/examples.md @@ -0,0 +1,246 @@ +# BIDS examples with empty raw data files + +Below are some examples of BIDS datasets that contain empty (example) raw data files. +These examples are separated by modality +and can assist you in converting your own dataset into a BIDS compliant dataset. + + + + + + + +### ASL + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:--------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------|:-----------------|:------------------------------------------|:------------------------------|:-----------------------------------------| +| [2d_mb_pcasl](https://github.com/bids-standard/bids-examples/tree/master/2d_mb_pcasl) | Siemens 2D MultiBand Multi-delay PCASL (m0 and noRF included within timeseries) | anat, fmap, perf | T1w, asl, aslcontext, epi | [link](https://osf.io/xrkc4/) | [@aptinis](https://github.com/aptinis) | +| [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 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) | + +### Behavioral + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------------------------|:---------------------------------------------------------------------------------------------------------------|:-------------------------------------------------|:-------------------------------------------| +| [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 | FLASH, T1w, 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 | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, 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) | + +### EEG + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------|:------------|:-----------------------------------------------|:------------------------------------------------|:-----------------------------------------------| +| [eeg_cbm](https://github.com/bids-standard/bids-examples/tree/master/eeg_cbm) | Rest EEG. European Data Format (.edf) | eeg | channels, eeg, events, scans | n/a | [@cpernet](https://github.com/cpernet) | +| [eeg_ds003645s_hed_library](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_library) | HED annotation using HED library vocabularies (schema). | eeg | channels, eeg, events | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | +| [eeg_face13](https://github.com/bids-standard/bids-examples/tree/master/eeg_face13) | Deconstructing the early visual electrocortical response to face and house stimuli. EDF format | eeg | channels, coordsystem, eeg, electrodes, events | n/a | [@andesha](https://github.com/andesha) | +| [eeg_matchingpennies](https://github.com/bids-standard/bids-examples/tree/master/eeg_matchingpennies) | Offline data of BCI experiment decoding left vs. right hand movement. BrainVision data format (.eeg, .vhdr, .vmrk) | eeg | channels, eeg, events | [link](https://doi.org/10.17605/OSF.IO/CJ2DR) | [@sappelhoff](https://github.com/sappelhoff) | +| [eeg_rishikesh](https://github.com/bids-standard/bids-examples/tree/master/eeg_rishikesh) | Mind wandering experiment. EEG data in Biosemi (.bdf) format | eeg | channels, eeg, events | [link](https://openneuro.org/datasets/ds001787) | [@arnodelorme](https://github.com/arnodelorme) | + +### DWI + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------|:--------------------------------|:---------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:-------------------------------------------| +| [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 | FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) | +| [ds114](https://github.com/bids-standard/bids-examples/tree/master/ds114) | multiple tasks, multiple runs | anat, dwi, func | T1w, bold, dwi, events | [link](https://openneuro.org/datasets/ds000114/versions/1.0.1) | n/a | +| [dwi_deriv](https://github.com/bids-standard/bids-examples/tree/master/dwi_deriv) | exemplifies the storage of diffusion MRI derivates that may be generated on the Siemens XA platform. | dwi | dwi | n/a | n/a | +| [eeg_rest_fmri](https://github.com/bids-standard/bids-examples/tree/master/eeg_rest_fmri) | Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk) | anat, dwi, eeg, func | T1w, bold, dwi, eeg | n/a | [@cpernet](https://github.com/cpernet) | +| [genetics_ukbb](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) | multiple tasks, T1w, DTI, BOLD, genetic info | anat, dwi, func | FLAIR, T1w, bold, dwi, events, info | n/a | [@cpernet](https://github.com/cpernet) | + +### iEEG + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------|:-----------------------|:-----------------------------------------------------------------------|:----------------------------------------------------------------------------|:---------------------------------------------| +| [ieeg_epilepsyNWB](https://github.com/bids-standard/bids-examples/tree/master/ieeg_epilepsyNWB) | multiple sessions, tutorial — derivative dataset of `ieeg_epilepsy` showcasing the NWB file format alternative | anat, ieeg | T1w, channels, coordsystem, electrodes, events, ieeg, scans | [link](https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap_bids) | [@TheChymera](https://github.com/TheChymera) | +| [ieeg_epilepsy](https://github.com/bids-standard/bids-examples/tree/master/ieeg_epilepsy) | multiple sessions, tutorial | anat, ieeg | T1w, channels, coordsystem, electrodes, events, ieeg, scans | [link](https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap_bids) | [@ftadel](https://github.com/ftadel) | +| [ieeg_epilepsy_ecog](https://github.com/bids-standard/bids-examples/tree/master/ieeg_epilepsy_ecog) | multiple sessions, tutorial | anat, ieeg | T1w, channels, coordsystem, electrodes, events, ieeg, photo, scans | [link](https://neuroimage.usc.edu/bst/getupdate.php?s=sample_ecog) | [@ftadel](https://github.com/ftadel) | +| [ieeg_filtered_speech](https://github.com/bids-standard/bids-examples/tree/master/ieeg_filtered_speech) | recordings of three seizures | ieeg | channels, coordsystem, electrodes, events, ieeg, photo | n/a | [@choldgraf](https://github.com/choldgraf) | +| [ieeg_motorMiller2007](https://github.com/bids-standard/bids-examples/tree/master/ieeg_motorMiller2007) | Cue-based hand & tongue movement data | ieeg | channels, coordsystem, electrodes, events, ieeg | n/a | [@dorahermes](https://github.com/dorahermes) | +| [ieeg_visual](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual) | Stimulus dependence of gamma oscillations in human visual cortex | anat, ieeg | T1w, channels, coordsystem, electrodes, events, ieeg | n/a | [@dorahermes](https://github.com/dorahermes) | +| [ieeg_visual_multimodal](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual_multimodal) | n/a | anat, fmap, func, ieeg | T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref | n/a | [@irisgroen](https://github.com/irisgroen) | +| [xeeg_hed_score](https://github.com/bids-standard/bids-examples/tree/master/xeeg_hed_score) | EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE | anat, eeg, ieeg | T1w, channels, coordsystem, eeg, electrodes, events, ieeg | n/a | [@dorahermes](https://github.com/dorahermes) | + +### HED + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------|:------------------------------------------------|:---------------------------------------------| +| [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 | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | +| [eeg_ds003645s_hed_library](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_library) | HED annotation using HED library vocabularies (schema). | eeg | channels, eeg, events | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | +| [xeeg_hed_score](https://github.com/bids-standard/bids-examples/tree/master/xeeg_hed_score) | EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE | anat, eeg, ieeg | T1w, channels, coordsystem, eeg, electrodes, events, ieeg | n/a | [@dorahermes](https://github.com/dorahermes) | + +### MEG + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:--------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------|:---------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:-------------------------------------------| +| [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 | FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) | +| [ds000246](https://github.com/bids-standard/bids-examples/tree/master/ds000246) | Auditory dataset used for Brainstorm’s general online tutorial | anat, meg | T1w, channels, coordsystem, headshape, meg, photo, scans | [link](https://openneuro.org/datasets/ds000246/versions/00001) | [@guiomar](https://github.com/guiomar) | +| [ds000247](https://github.com/bids-standard/bids-examples/tree/master/ds000247) | Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA). | anat, meg | T1w, channels, coordsystem, headshape, meg, scans | [link](https://openneuro.org/datasets/ds000247/versions/00001) | [@guiomar](https://github.com/guiomar) | +| [ds000248](https://github.com/bids-standard/bids-examples/tree/master/ds000248) | MNE sample data: Data with visual and auditory stimuli | anat, meg | FLASH, T1w, channels, coordsystem, events, meg, scans | [link](https://openneuro.org/datasets/ds000248/versions/00001) | [@agramfort](https://github.com/agramfort) | + +### Microscopy + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------|:---------------------------------------------| +| [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 | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | +| [micr_SEM](https://github.com/bids-standard/bids-examples/tree/master/micr_SEM) | Example SEM dataset in PNG format with 1 sample imaged over 2 sessions | micr | SEM, photo, samples, sessions | [link](https://doi.org/10.5281/zenodo.5498378) | [@jcohenadad](https://github.com/jcohenadad) | +| [micr_SEMzarr](https://github.com/bids-standard/bids-examples/tree/master/micr_SEMzarr) | Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions | micr | SEM, SPIM, samples, sessions | n/a | [@TheChymera](https://github.com/TheChymera) | +| [micr_SPIM](https://github.com/bids-standard/bids-examples/tree/master/micr_SPIM) | Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each | micr | SPIM, photo, samples | [link](https://doi.org/10.5281/zenodo.5517223) | [@jcohenadad](https://github.com/jcohenadad) | +| [micr_XPCTzarr](https://github.com/bids-standard/bids-examples/tree/master/micr_XPCTzarr) | Example XPCT dataset in OME-ZARR format with 1 sample imaged | micr | XPCT, photo, samples, sessions | [link](https://human-organ-atlas.esrf.eu/datasets/572252538) | [@chourroutm](https://github.com/chourroutm) | + +### Motion + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:--------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------|:-------------------------------------------------| +| [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 | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | +| [motion_dualtask](https://github.com/bids-standard/bids-examples/tree/master/motion_dualtask) | older and younger participants walking while performing discrimination task | eeg, motion | channels, eeg, events, motion, scans | n/a | [@sjeung](https://github.com/sjeung) | +| [motion_spotrotation](https://github.com/bids-standard/bids-examples/tree/master/motion_spotrotation) | participants rotated heading using full-body motion or joystick | eeg, motion | channels, coordsystem, eeg, electrodes, events, motion, scans | [link](https://openneuro.org/datasets/ds004460) | [@sjeung](https://github.com/sjeung) | +| [motion_systemvalidation](https://github.com/bids-standard/bids-examples/tree/master/motion_systemvalidation) | Example dataset of two different motion captured system recorded almost simultaneously, but no brain data | motion | channels, motion, scans | [link](https://doi.org/10.6084/m9.figshare.20238006.v2) | [@JuliusWelzel](https://github.com/JuliusWelzel) | + +### MRI + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------------------------|:---------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:-------------------------------------------| +| [7t_trt](https://github.com/bids-standard/bids-examples/tree/master/7t_trt) | n/a | anat, fmap, func | T1map, T1w, bold, magnitude1, magnitude2, phasediff, physio, scans, sessions | [link](https://bit.ly/2H0Z6Qt) | n/a | +| [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 | FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) | +| [ds001](https://github.com/bids-standard/bids-examples/tree/master/ds001) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000001/versions/00006) | n/a | +| [ds002](https://github.com/bids-standard/bids-examples/tree/master/ds002) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000002/versions/00002) | n/a | +| [ds003](https://github.com/bids-standard/bids-examples/tree/master/ds003) | single task, single run | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000003/versions/00001) | n/a | +| [ds005](https://github.com/bids-standard/bids-examples/tree/master/ds005) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000005/versions/00001) | n/a | +| [ds006](https://github.com/bids-standard/bids-examples/tree/master/ds006) | single task, multiple sessions, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000006/versions/00001) | n/a | +| [ds007](https://github.com/bids-standard/bids-examples/tree/master/ds007) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000007/versions/00001) | n/a | +| [ds008](https://github.com/bids-standard/bids-examples/tree/master/ds008) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000008/versions/00001) | n/a | +| [ds009](https://github.com/bids-standard/bids-examples/tree/master/ds009) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2, scans | [link](https://openneuro.org/datasets/ds000009/versions/00002) | n/a | +| [ds011](https://github.com/bids-standard/bids-examples/tree/master/ds011) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000011/versions/00001) | n/a | +| [ds051](https://github.com/bids-standard/bids-examples/tree/master/ds051) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000051/versions/00001) | n/a | +| [ds052](https://github.com/bids-standard/bids-examples/tree/master/ds052) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000052/versions/00001) | n/a | +| [ds101](https://github.com/bids-standard/bids-examples/tree/master/ds101) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000101/versions/00004) | n/a | +| [ds102](https://github.com/bids-standard/bids-examples/tree/master/ds102) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000102/versions/00001) | n/a | +| [ds105](https://github.com/bids-standard/bids-examples/tree/master/ds105) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000105/versions/00001) | n/a | +| [ds107](https://github.com/bids-standard/bids-examples/tree/master/ds107) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000107/versions/00001) | n/a | +| [ds108](https://github.com/bids-standard/bids-examples/tree/master/ds108) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000108/versions/00002) | n/a | +| [ds109](https://github.com/bids-standard/bids-examples/tree/master/ds109) | multiple tasks, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000109/versions/00001) | n/a | +| [ds110](https://github.com/bids-standard/bids-examples/tree/master/ds110) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000110/versions/00001) | n/a | +| [ds113b](https://github.com/bids-standard/bids-examples/tree/master/ds113b) | forrest gump watching, multiple sessions, multiple runs | func | bold, events | [link](https://openneuro.org/datasets/ds000113/versions/1.3.0) | n/a | +| [ds114](https://github.com/bids-standard/bids-examples/tree/master/ds114) | multiple tasks, multiple runs | anat, dwi, func | T1w, bold, dwi, events | [link](https://openneuro.org/datasets/ds000114/versions/1.0.1) | n/a | +| [ds116](https://github.com/bids-standard/bids-examples/tree/master/ds116) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000116/versions/00003) | n/a | +| [ds210](https://github.com/bids-standard/bids-examples/tree/master/ds210) | multiple tasks, multiple runs | func | bold, physio | [link](https://openneuro.org/datasets/ds000210/versions/00002) | n/a | +| [eeg_rest_fmri](https://github.com/bids-standard/bids-examples/tree/master/eeg_rest_fmri) | Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk) | anat, dwi, eeg, func | T1w, bold, dwi, eeg | n/a | [@cpernet](https://github.com/cpernet) | +| [genetics_ukbb](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) | multiple tasks, T1w, DTI, BOLD, genetic info | anat, dwi, func | FLAIR, T1w, bold, dwi, events, info | n/a | [@cpernet](https://github.com/cpernet) | +| [ieeg_visual_multimodal](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual_multimodal) | n/a | anat, fmap, func, ieeg | T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref | n/a | [@irisgroen](https://github.com/irisgroen) | +| [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) | + +### MRS + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:--------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------|:------------|:-------------------------|:-------------------------------------------------|:---------------------------------------------------| +| [mrs_2dmrsi](https://github.com/bids-standard/bids-examples/tree/master/mrs_2dmrsi) | 2D sLASER MRSI data from 8 subjects | anat, mrs | T1w, mrsi | [link](https://zenodo.org/records/7701228) | [@markmikkelsen](https://github.com/markmikkelsen) | +| [mrs_biggaba](https://github.com/bids-standard/bids-examples/tree/master/mrs_biggaba) | MEGA-PRESS and PRESS MRS data from 12 subjects from one site from the Big GABA project | anat, mrs | T1w, mrsref, svs | [link](https://www.nitrc.org/projects/biggaba) | [@markmikkelsen](https://github.com/markmikkelsen) | +| [mrs_fmrs](https://github.com/bids-standard/bids-examples/tree/master/mrs_fmrs) | Functional MRS data involving a pain stimulus task from 15 subjects | anat, mrs | T1w, events, mrsref, svs | [link](https://www.nitrc.org/projects/fmrs_2020) | [@markmikkelsen](https://github.com/markmikkelsen) | + +### NIRS + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:----------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------|:------------|:---------------------------------------------------------------------|:-----------------------------------------------|:---------------------------------------------------------| +| [fnirs_automaticity](https://github.com/bids-standard/bids-examples/tree/master/fnirs_automaticity) | 24 subjects performing (non-)automatic finger tapping and foot stepping | nirs | channels, coordsystem, events, nirs, optodes, practicelogbook, scans | [link](https://doi.org/10.34973/vesb-mh30) | [@robertoostenveld](https://github.com/robertoostenveld) | +| [fnirs_tapping](https://github.com/bids-standard/bids-examples/tree/master/fnirs_tapping) | Example fNIRS measurement with three conditions from five subjects | nirs | channels, coordsystem, events, nirs, optodes, scans | [link](https://doi.org/10.5281/zenodo.5529797) | [@rob-luke](https://github.com/rob-luke) | + +### PET + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:----------------------------------------------------------------------------|:----------------|:------------|:-----------------|:-------------------------------------------------|:---------------------------------------------| +| [pet001](https://github.com/bids-standard/bids-examples/tree/master/pet001) | T1w, PET, blood | anat, pet | T1w, blood, pet | n/a | [@mnoergaard](https://github.com/mnoergaard) | +| [pet002](https://github.com/bids-standard/bids-examples/tree/master/pet002) | T1w, PET | anat, pet | T1w, pet | [link](https://openneuro.org/datasets/ds001420/) | [@mnoergaard](https://github.com/mnoergaard) | +| [pet003](https://github.com/bids-standard/bids-examples/tree/master/pet003) | T1w, PET, blood | anat, pet | T1w, blood, pet | n/a | [@mnoergaard](https://github.com/mnoergaard) | +| [pet004](https://github.com/bids-standard/bids-examples/tree/master/pet004) | PET, blood | pet | blood, pet | n/a | [@mnoergaard](https://github.com/mnoergaard) | +| [pet005](https://github.com/bids-standard/bids-examples/tree/master/pet005) | T1w, PET | anat, pet | T1w, events, pet | n/a | [@mnoergaard](https://github.com/mnoergaard) | + +### qMRI + + + +| 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 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, T1map, UNIT1, 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 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) | diff --git a/docs/datasets/index.md b/docs/datasets/index.md index 0041d09c..6b7b7c82 100644 --- a/docs/datasets/index.md +++ b/docs/datasets/index.md @@ -33,205 +33,3 @@ to BIDS format are provided. ## Mother of unification studies A 204-subject multimodal (MEG, MRI, fMRI) [dataset](http://data.donders.ru.nl/collections/di/dccn/DSC_3011020.09_236?0) to study language processing. - -## BIDS examples with empty raw data files -Below are some examples of BIDS datasets that contain empty (example) raw data files. These examples -are separated by modality and can assist you in converting your own dataset into a BIDS compliant -dataset. - - - - - - - -### ASL - - - -| name | description | datatypes | suffixes | link to full data | maintained by | -|:----------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------|:-----------------|:------------------------------------------|:------------------------------|:-----------------------------------------| -| [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 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 - - - -| name | description | datatypes | suffixes | link to full data | maintained by | -|:------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------|:------------|:-----------------------------------------------|:------------------------------------------------|:-----------------------------------------------| -| [eeg_cbm](https://github.com/bids-standard/bids-examples/tree/master/eeg_cbm) | Rest EEG. European Data Format (.edf) | eeg | channels, eeg, events, scans | n/a | [@cpernet](https://github.com/cpernet) | -| [eeg_ds003645s_hed_library](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_library) | HED annotation using HED library vocabularies (schema). | eeg | channels, eeg, events | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | -| [eeg_face13](https://github.com/bids-standard/bids-examples/tree/master/eeg_face13) | Deconstructing the early visual electrocortical response to face and house stimuli. EDF format | eeg | channels, coordsystem, eeg, electrodes, events | n/a | [@andesha](https://github.com/andesha) | -| [eeg_matchingpennies](https://github.com/bids-standard/bids-examples/tree/master/eeg_matchingpennies) | Offline data of BCI experiment decoding left vs. right hand movement. BrainVision data format (.eeg, .vhdr, .vmrk) | eeg | channels, eeg, events | [link](https://doi.org/10.17605/OSF.IO/CJ2DR) | [@sappelhoff](https://github.com/sappelhoff) | -| [eeg_rishikesh](https://github.com/bids-standard/bids-examples/tree/master/eeg_rishikesh) | Mind wandering experiment. EEG data in Biosemi (.bdf) format | eeg | channels, eeg, events | [link](https://openneuro.org/datasets/ds001787) | [@arnodelorme](https://github.com/arnodelorme) | - -### iEEG - - - -| name | description | datatypes | suffixes | link to full data | maintained by | -|:------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------|:-----------------------|:-----------------------------------------------------------------------|:----------------------------------------------------------------------------|:---------------------------------------------| -| [ieeg_epilepsyNWB](https://github.com/bids-standard/bids-examples/tree/master/ieeg_epilepsyNWB) | multiple sessions, tutorial — derivative dataset of `ieeg_epilepsy` showcasing the NWB file format alternative | anat, ieeg | T1w, channels, coordsystem, electrodes, events, ieeg, scans | [link](https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap_bids) | [@TheChymera](https://github.com/TheChymera) | -| [ieeg_epilepsy](https://github.com/bids-standard/bids-examples/tree/master/ieeg_epilepsy) | multiple sessions, tutorial | anat, ieeg | T1w, channels, coordsystem, electrodes, events, ieeg, scans | [link](https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap_bids) | [@ftadel](https://github.com/ftadel) | -| [ieeg_epilepsy_ecog](https://github.com/bids-standard/bids-examples/tree/master/ieeg_epilepsy_ecog) | multiple sessions, tutorial | anat, ieeg | T1w, channels, coordsystem, electrodes, events, ieeg, photo, scans | [link](https://neuroimage.usc.edu/bst/getupdate.php?s=sample_ecog) | [@ftadel](https://github.com/ftadel) | -| [ieeg_filtered_speech](https://github.com/bids-standard/bids-examples/tree/master/ieeg_filtered_speech) | recordings of three seizures | ieeg | channels, coordsystem, electrodes, events, ieeg, photo | n/a | [@choldgraf](https://github.com/choldgraf) | -| [ieeg_motorMiller2007](https://github.com/bids-standard/bids-examples/tree/master/ieeg_motorMiller2007) | Cue-based hand & tongue movement data | ieeg | channels, coordsystem, electrodes, events, ieeg | n/a | [@dorahermes](https://github.com/dorahermes) | -| [ieeg_visual](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual) | Stimulus dependence of gamma oscillations in human visual cortex | anat, ieeg | T1w, channels, coordsystem, electrodes, events, ieeg | n/a | [@dorahermes](https://github.com/dorahermes) | -| [ieeg_visual_multimodal](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual_multimodal) | n/a | anat, fmap, func, ieeg | T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref | n/a | [@irisgroen](https://github.com/irisgroen) | - -### MEG - - - -| name | description | datatypes | suffixes | link to full data | maintained by | -|:--------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------|:------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:-------------------------------------------| -| [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 | FLASH, T1w, beh, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) | -| [ds000246](https://github.com/bids-standard/bids-examples/tree/master/ds000246) | Auditory dataset used for Brainstorm’s general online tutorial | anat, meg | ChannelGroupSet, ClassFile, MarkerFile, T1w, channels, coordsystem, default, headshape, meg, params, photo, processing, scans | [link](https://openneuro.org/datasets/ds000246/versions/00001) | [@guiomar](https://github.com/guiomar) | -| [ds000247](https://github.com/bids-standard/bids-examples/tree/master/ds000247) | Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA). | anat, meg | ClassFile, T1w, bad, channels, coordsystem, default, headshape, meg, params, processing, scans | [link](https://openneuro.org/datasets/ds000247/versions/00001) | [@guiomar](https://github.com/guiomar) | -| [ds000248](https://github.com/bids-standard/bids-examples/tree/master/ds000248) | MNE sample data: Data with visual and auditory stimuli | anat, meg | FLASH, T1w, channels, coordsystem, events, meg, scans | [link](https://openneuro.org/datasets/ds000248/versions/00001) | [@agramfort](https://github.com/agramfort) | - -### Microscopy - - - -| name | description | datatypes | suffixes | link to full data | maintained by | -|:------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------|:-----------------------------|:--------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------|:---------------------------------------------| -| [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 | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, headshape, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | -| [micr_SEM](https://github.com/bids-standard/bids-examples/tree/master/micr_SEM) | Example SEM dataset in PNG format with 1 sample imaged over 2 sessions | micr | SEM, photo, samples, sessions | [link](https://doi.org/10.5281/zenodo.5498378) | [@jcohenadad](https://github.com/jcohenadad) | -| [micr_SEMzarr](https://github.com/bids-standard/bids-examples/tree/master/micr_SEMzarr) | Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions | micr | SEM, SPIM, samples, sessions | n/a | [@TheChymera](https://github.com/TheChymera) | -| [micr_SPIM](https://github.com/bids-standard/bids-examples/tree/master/micr_SPIM) | Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each | micr | SPIM, photo, samples | [link](https://doi.org/10.5281/zenodo.5517223) | [@jcohenadad](https://github.com/jcohenadad) | - -### Motion - - - -| name | description | datatypes | suffixes | link to full data | maintained by | -|:--------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------|:-----------------------------|:--------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------|:-------------------------------------------------| -| [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 | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, headshape, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | -| [motion_dualtask](https://github.com/bids-standard/bids-examples/tree/master/motion_dualtask) | older and younger participants walking while performing discrimination task | eeg, motion | channels, eeg, events, motion, scans | n/a | [@sjeung](https://github.com/sjeung) | -| [motion_spotrotation](https://github.com/bids-standard/bids-examples/tree/master/motion_spotrotation) | participants rotated heading using full-body motion or joystick | eeg, motion | channels, coordsystem, eeg, electrodes, events, motion, scans | [link](https://openneuro.org/datasets/ds004460) | [@sjeung](https://github.com/sjeung) | -| [motion_systemvalidation](https://github.com/bids-standard/bids-examples/tree/master/motion_systemvalidation) | Example dataset of two different motion captured system recorded almost simultaneously, but no brain data | motion | channels, motion, scans | [link](https://doi.org/10.6084/m9.figshare.20238006.v2) | [@JuliusWelzel](https://github.com/JuliusWelzel) | - -### MRI - - - -| name | description | datatypes | suffixes | link to full data | maintained by | -|:------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------------------------|:--------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:-------------------------------------------| -| [7t_trt](https://github.com/bids-standard/bids-examples/tree/master/7t_trt) | n/a | anat, fmap, func | T1map, T1w, bold, magnitude1, magnitude2, phasediff, physio, scans, sessions | [link](https://bit.ly/2H0Z6Qt) | n/a | -| [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 | FLASH, T1w, beh, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) | -| [ds001](https://github.com/bids-standard/bids-examples/tree/master/ds001) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000001/versions/00006) | n/a | -| [ds002](https://github.com/bids-standard/bids-examples/tree/master/ds002) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000002/versions/00002) | n/a | -| [ds003](https://github.com/bids-standard/bids-examples/tree/master/ds003) | single task, single run | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000003/versions/00001) | n/a | -| [ds005](https://github.com/bids-standard/bids-examples/tree/master/ds005) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000005/versions/00001) | n/a | -| [ds006](https://github.com/bids-standard/bids-examples/tree/master/ds006) | single task, multiple sessions, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000006/versions/00001) | n/a | -| [ds007](https://github.com/bids-standard/bids-examples/tree/master/ds007) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000007/versions/00001) | n/a | -| [ds008](https://github.com/bids-standard/bids-examples/tree/master/ds008) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000008/versions/00001) | n/a | -| [ds009](https://github.com/bids-standard/bids-examples/tree/master/ds009) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2, scans | [link](https://openneuro.org/datasets/ds000009/versions/00002) | n/a | -| [ds011](https://github.com/bids-standard/bids-examples/tree/master/ds011) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000011/versions/00001) | n/a | -| [ds051](https://github.com/bids-standard/bids-examples/tree/master/ds051) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000051/versions/00001) | n/a | -| [ds052](https://github.com/bids-standard/bids-examples/tree/master/ds052) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000052/versions/00001) | n/a | -| [ds101](https://github.com/bids-standard/bids-examples/tree/master/ds101) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000101/versions/00004) | n/a | -| [ds102](https://github.com/bids-standard/bids-examples/tree/master/ds102) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000102/versions/00001) | n/a | -| [ds105](https://github.com/bids-standard/bids-examples/tree/master/ds105) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000105/versions/00001) | n/a | -| [ds107](https://github.com/bids-standard/bids-examples/tree/master/ds107) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000107/versions/00001) | n/a | -| [ds108](https://github.com/bids-standard/bids-examples/tree/master/ds108) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000108/versions/00002) | n/a | -| [ds109](https://github.com/bids-standard/bids-examples/tree/master/ds109) | multiple tasks, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000109/versions/00001) | n/a | -| [ds110](https://github.com/bids-standard/bids-examples/tree/master/ds110) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000110/versions/00001) | n/a | -| [ds113b](https://github.com/bids-standard/bids-examples/tree/master/ds113b) | forrest gump watching, multiple sessions, multiple runs | func | bold, events | [link](https://openneuro.org/datasets/ds000113/versions/1.3.0) | n/a | -| [ds114](https://github.com/bids-standard/bids-examples/tree/master/ds114) | multiple tasks, multiple runs | anat, dwi, func | T1w, bold, dwi, events | [link](https://openneuro.org/datasets/ds000114/versions/1.0.1) | n/a | -| [ds116](https://github.com/bids-standard/bids-examples/tree/master/ds116) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000116/versions/00003) | n/a | -| [ds210](https://github.com/bids-standard/bids-examples/tree/master/ds210) | multiple tasks, multiple runs | func | bold, physio | [link](https://openneuro.org/datasets/ds000210/versions/00002) | n/a | -| [eeg_rest_fmri](https://github.com/bids-standard/bids-examples/tree/master/eeg_rest_fmri) | Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk) | anat, dwi, eeg, func | T1w, bold, dwi, eeg | n/a | [@cpernet](https://github.com/cpernet) | -| [genetics_ukbb](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) | multiple tasks, T1w, DTI, BOLD, genetic info | anat, dwi, func | FLAIR, T1w, bold, dwi, events, info | n/a | [@cpernet](https://github.com/cpernet) | -| [ieeg_visual_multimodal](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual_multimodal) | n/a | anat, fmap, func, ieeg | T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref | n/a | [@irisgroen](https://github.com/irisgroen) | -| [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) | - -### NIRS - - - -| name | description | datatypes | suffixes | link to full data | maintained by | -|:----------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------|:------------|:---------------------------------------------------------------------|:-----------------------------------------------|:---------------------------------------------------------| -| [fnirs_automaticity](https://github.com/bids-standard/bids-examples/tree/master/fnirs_automaticity) | 24 subjects performing (non-)automatic finger tapping and foot stepping | nirs | channels, coordsystem, events, nirs, optodes, practicelogbook, scans | [link](https://doi.org/10.34973/vesb-mh30) | [@robertoostenveld](https://github.com/robertoostenveld) | -| [fnirs_tapping](https://github.com/bids-standard/bids-examples/tree/master/fnirs_tapping) | Example fNIRS measurement with three conditions from five subjects | nirs | channels, coordsystem, events, nirs, optodes, scans | [link](https://doi.org/10.5281/zenodo.5529797) | [@rob-luke](https://github.com/rob-luke) | - -### PET - - - -| name | description | datatypes | suffixes | link to full data | maintained by | -|:----------------------------------------------------------------------------|:----------------|:------------|:-----------------|:-------------------------------------------------|:---------------------------------------------| -| [pet001](https://github.com/bids-standard/bids-examples/tree/master/pet001) | T1w, PET, blood | anat, pet | T1w, blood, pet | n/a | [@mnoergaard](https://github.com/mnoergaard) | -| [pet002](https://github.com/bids-standard/bids-examples/tree/master/pet002) | T1w, PET | anat, pet | T1w, pet | [link](https://openneuro.org/datasets/ds001420/) | [@mnoergaard](https://github.com/mnoergaard) | -| [pet003](https://github.com/bids-standard/bids-examples/tree/master/pet003) | T1w, PET, blood | anat, pet | T1w, blood, pet | n/a | [@mnoergaard](https://github.com/mnoergaard) | -| [pet004](https://github.com/bids-standard/bids-examples/tree/master/pet004) | PET, blood | pet | blood, pet | n/a | [@mnoergaard](https://github.com/mnoergaard) | -| [pet005](https://github.com/bids-standard/bids-examples/tree/master/pet005) | T1w, PET | anat, pet | T1w, events, pet | n/a | [@mnoergaard](https://github.com/mnoergaard) | - -### qMRI - - - -| 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 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, T1map, UNIT1, 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 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 - - - -| name | description | datatypes | suffixes | link to full data | maintained by | -|:------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------------------------|:--------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------|:-------------------------------------------| -| [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 | FLASH, 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 | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, headshape, motion, photo, samples, 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) | diff --git a/makefile b/makefile index dc4e25f2..1693697e 100644 --- a/makefile +++ b/makefile @@ -21,7 +21,7 @@ update_contributors: package.json update_datasets_examples: @echo " ---------------------------------- " - python data/datasets/examples/tools/print_dataset_listing.py docs/datasets/index.md + python data/datasets/examples/tools/print_dataset_listing.py docs/datasets/examples.md # Figures diff --git a/mkdocs.yml b/mkdocs.yml index c38d0d07..859fea28 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -143,6 +143,7 @@ nav: - tools/converters.md - Datasets: - datasets/index.md + - datasets/examples.md - FAQ: - faq/index.md - faq/general.md diff --git a/specification b/specification index 47240837..f839a276 160000 --- a/specification +++ b/specification @@ -1 +1 @@ -Subproject commit 4724083745155d56b85cd909e8287dc6d6b42f64 +Subproject commit f839a276a0916a1f74ff2c4f92e72a5fdb7e1e20 From 5be2250ceda0389ec84e49ba62ba4f422e648a3b Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 12 Nov 2024 09:06:17 +0100 Subject: [PATCH 2/7] [ENH] update bids examples page (#573) --- data/datasets/examples | 2 +- docs/datasets/examples.md | 9 ++++----- docs/datasets/index.md | 6 ++++++ 3 files changed, 11 insertions(+), 6 deletions(-) diff --git a/data/datasets/examples b/data/datasets/examples index 2f634a14..507df662 160000 --- a/data/datasets/examples +++ b/data/datasets/examples @@ -1 +1 @@ -Subproject commit 2f634a14681587408a7c00f7dfbf6b22dba1e327 +Subproject commit 507df6626dbbc555ae258ae286885d0a1b18391c diff --git a/docs/datasets/examples.md b/docs/datasets/examples.md index 36edfcb0..bdbfe4ba 100644 --- a/docs/datasets/examples.md +++ b/docs/datasets/examples.md @@ -1,9 +1,8 @@ -# BIDS examples with empty raw data files - -Below are some examples of BIDS datasets that contain empty (example) raw data files. -These examples are separated by modality -and can assist you in converting your own dataset into a BIDS compliant dataset. +# BIDS examples +[BIDS examples datasets](./examples.md) contain empty (example) raw data files +and can assist you in converting your own dataset into a BIDS compliant dataset, +or to run some tests with your code... diff --git a/docs/datasets/index.md b/docs/datasets/index.md index 6b7b7c82..cd16473e 100644 --- a/docs/datasets/index.md +++ b/docs/datasets/index.md @@ -33,3 +33,9 @@ to BIDS format are provided. ## Mother of unification studies A 204-subject multimodal (MEG, MRI, fMRI) [dataset](http://data.donders.ru.nl/collections/di/dccn/DSC_3011020.09_236?0) to study language processing. + +## BIDS examples with empty raw data files + +[BIDS examples datasets](./examples.md) contain empty (example) raw data files +and can assist you in converting your own dataset into a BIDS compliant dataset, +or to run some tests with your code... From 19d14f4d85bd6601b8910744be926a51b2c80310 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Wed, 13 Nov 2024 13:50:33 -0500 Subject: [PATCH 3/7] BLOG: Add bids-validator 2.0 announcement (#575) --- docs/blog/posts/bids-validator-2.0.md | 447 ++++++++++++++++++++++++++ 1 file changed, 447 insertions(+) create mode 100644 docs/blog/posts/bids-validator-2.0.md diff --git a/docs/blog/posts/bids-validator-2.0.md b/docs/blog/posts/bids-validator-2.0.md new file mode 100644 index 00000000..a117ea76 --- /dev/null +++ b/docs/blog/posts/bids-validator-2.0.md @@ -0,0 +1,447 @@ +--- +date: 2024-11-13 +slug: bids-validator-2 +author: Chris Markiewicz +categories: +- validator +- schema +- news +--- + +# BIDS Validator 2.0 + +We are pleased to announce the release of version 2.0 of the BIDS Validator. + +In the last few months, you may have noticed changes to the validator available at +, including the look and feel of the +validator, the errors and warnings that are produced by the validator, +and a link to a "legacy validator". +In this blog post, we'll explain what all this means and how to use the new validator. + + + +## Background + +One of the primary goals of the BIDS validator was to make it easy to validate a BIDS +dataset, regardless of the user's operating system. By using Javascript and hosting a web +app that ran entirely in the user's browser, we were able to achieve this goal without +requiring users to install anything. This decision was crucial to the success of the validator, +which in turn was crucial to the success of BIDS. + +This decision came at a cost, however. While programming expertise and open source development +are prevalent and valued in the neuroimaging community, most of that expertise is in Python, +R and MATLAB (and to some extent C/C++), and relatively few researchers have much experience +with Javascript. As a result, as BIDS grew with BIDS Extension Proposals (BEPs), updating the +validator to support the new data types and enforce the new rules became a consistent +bottleneck. + +### The BIDS Schema + +In the summer of 2021, the BIDS [Steering Group][] approved the development of the BIDS Schema, +a project to encode as much of the BIDS Standard as possible in declarative, +machine-readable rules, and to rewrite the validator to use the schema to enforce the rules. +This would have several advantages: + +1. A schema could be updated by BIDS contributors without knowledge of Javascript or an + understanding of the structure of the BIDS Validator code base. + +1. A language agnostic schema would enable validators to be written in other languages, + or for other tools to be written in a way where updates to BIDS could be automatically + incorporated by upgrading the schema. + +1. By using the schema as an authoritative source of definitions, + large portions of the *text* of the BIDS specification could be generated automatically, + and with less chance for inconsistency. + +A description of the BIDS schema can be found in the [bidsschematools][bst desc] documentation, +and the schema itself may be found at +. +(Replace `latest` with a particular version, for example, +`v1.10.0`, to find a snapshot of the schema at the time of that release.) + +## The Schema Validator + +The schema validator is now feature complete, validating file names, +JSON file fields and values, TSV file column names and values, +and various [checks] that have been written in the schema expression language. + +To use the schema validator, visit +or download the [Deno] Javascript runtime and run: + +```console +deno run -A jsr:@bids/validator [PATH] +``` + +While many features of the original BIDS validator have been preserved, +the structure of JSON configuration files and JSON outputs +(triggered by the `--json` flag) have changed their formats. +Advanced users may need to update their tooling on either end. + +### New features + +The schema validator includes features that were never implemented in the +legacy validator: + +- Validation of [BIDS Derivatives] (introduced in BIDS 1.4.0) datasets, + including opt-in recursive validation of BIDS Derivatives datasets discovered in + `derivatives/` subdirectories. + +- Support for [BIDS-MRS] (Magnetic Resonance Spectroscopy), + introduced in BIDS 1.10.0. + +### Behavior changes + +- The [inheritance principle][] is consistently applied for all files. + For example, a top-level `bold.json` was previously singled out to be + invalid without a `task` entity. + +- Every JSON field or TSV column defined in BIDS is type-checked against the + schema definitions used to produce the tables in the specification. + (For example, [`FlipAngle`][flipangle] is verified to be a number, rather + than a string with a degree symbol.) + Improved conformity reduces the scope for inconsistency for downstream tools + to accommodate. + +- Extra metadata is no longer prohibited in sidecar JSON files, which was + inconsistently applied across data types in the legacy validator. + +- All RECOMMENDED fields produce a warning if absent. + +Some of these changes may not be to everyone's taste, +but we believe that consistent application of the specification is critical +to the utility of BIDS and the maintainability of the validator. +We hope that a consistent validator will help inform future changes to BIDS, +so that the specification can get closer to the needs and preferences +of the community. + +### Development validator + +The BIDS Validator tracks the latest release of the BIDS specification (currently [v1.10.0]). +As the next release of BIDS is developed, changes to the schema or the validator may be +tested at . + +Note that any changes in this validator may be reverted prior to the next release of BIDS. +Command-line use of the development validator is not currently supported. + +### Updated documentation + +The original BIDS validator had limited documentation, +primarily a README that was replicated on GitHub and [NPM][npm:validator]. +For the 2.0 release of the validator, we've added documentation at +. + +In addition to user guides for the [web][web-validator] and [command-line] interfaces +to the validator, we aim to include more detail on the operation of the validator, +starting with the [validation model][]. +Our goal is to demystify the validator and the BIDS Schema and empower researchers and +developers to adapt and reuse the tools we've built. + +This site is under active development, and will be updated frequently in the +coming weeks. Please help us improve it by opening issues (or PRs)! + +## Questions + +### Q1. My dataset was valid with the old validator but it is not anymore. Why? Which one should I trust? + +The validator has been completely reimplemented and shares no code with the +original validator. A new failure could mean a bug in the new validator, but +it is more likely to indicate a blind spot in the legacy validator. For +example, the legacy validator spot-checked many JSON sidecar fields with custom +code; in contrast, the schema validator systematically checks every sidecar +field for applicability, and validates the types of the values according to the +definitions in the schema. + +### Q2. Can I continue using the legacy validator? + +Yes, but there are no plans to continue maintaining the legacy validator. +Its behavior will inevitably diverge further from that of the schema validator, +and eventually it will be difficult to get the validator to run, +as the Node.js ecosystem moves on. +The Docker images will continue to work for longer. + +We recommend migrating to the schema validator sooner than later, +and report any bugs you find in the process. + +### Q3. Where should I report bugs? + +The same place as ever: + +Note that in some cases the fixes for the bugs will be in the specification +itself, as the bug may be in the schema-defined rules that the validator is +applying. + +### Q4. What about the Docker image? + +The [bids/validator](https://hub.docker.com/r/bids/validator/) image +still contains the legacy validator, as of version 1.15.0. +Compared to Node.js, the Deno runtime removes most of the complicated parts +of package installation, which reduces the benefit-to-cost ratio for +containerization. +However, if you see version 2.0 or higher, it will be the schema validator. + +The [bids/base_validator](https://hub.docker.com/r/bids/base_validator/) +image contains the schema validator, as of version 1.15.0. +This image is intended for building BIDS Apps that pre-validate the +dataset, but can also be used with: + +```shell +docker run --rm -it --platform linux/amd64 -v $DATASET:/data bids/base_validator \ + bids-validator /data +``` + +## Some technical details + +In this section, we lay out some details that are probably not of general interest, +but could be useful for understanding the changes to validator behavior, +the validation resources available, and the planned maintenance levels. + +### Evolution of the specification and validators + +#### In the beginning… + +
+ +```mermaid +graph LR; + subgraph bids-specification; + google["Google Doc"] + end + subgraph "bids-validator"; + regex["filename patterns"] --> Node.js + regex["filename patterns"] ---> python + Node.js --> web + end + + google -. interpreted .-> regex +``` + +The original validator was an interpretation of a pure text specification. +The filename patterns were shared between the full Node.JS validator +and a minimal Python validator. + +
+ +The BIDS specification was a Google Document and the validator implemented every +rule with a custom Javascript function. +For validating file names, a hand-curated list of [regular expressions] were used +by both the Javascript validator and a small Python library ([bids-validator][py]). + +In 2018, the specification was transitioned to a [Markdown] site, +hosted at [bids-standard/bids-specification]. + +
+ +```mermaid +graph LR; + subgraph bids-specification; + markdown ---> specification + end + subgraph "bids-validator"; + regex["filename patterns"] --> Node.js + regex["filename patterns"] ---> python + Node.js --> web + end + + specification -. interpreted .-> regex +``` + +The transition to a git-managed Markdown document initially made +change-tracking and contribution to the specification more transparent. + +
+ +#### v1.14.6 + +
+ +```mermaid +graph LR; + subgraph bids-specification; + markdown ---> specification + schema --> bidsschematools --> specification & schema.json + end + subgraph "bids-validator @ v1.14.6"; + regex["filename patterns"] --> Node.js + regex["filename patterns"] --> python + Node.js --> web + deno + end + + specification -. interpreted .-> regex + schema.json ---> deno +``` + +The BIDS schema is used as an authoritative, +machine-readable source for the specification text and tools wishing +to work with BIDS terms. +Node.js, Python and Deno validators coexisted in a single repository. + +
+ +Recently, the [bids-standard/bids-specification][] repository has hosted the Markdown +source code of the specification and the [bidsschematools][] package. +This package compiles the schema from its YAML source into a single JSON blob, +which is used for rendering the specification document and producing the +canonical `schema.json` file that can be reused. + +In the [bids-standard/bids-validator][] repository, the Python and Javascript validators have +continued to coexist, along with a new validator that is written to apply the +schema, and targeting the [Deno] Javascript runtime. + +#### v1.14.7 + +
+ +```mermaid +graph LR; + subgraph bids-specification; + markdown ---> specification + schema --> bidsschematools --> specification & schema.json + end + subgraph "bids-validator @ v1.14.7"; + regex["filename patterns"] --> Node.js + Node.js --> web + deno + python + end + + specification -. interpreted .-> regex + schema.json ---> deno + bidsschematools ----> python +``` + + +To prepare for separation, the Python validator dependency on the +shared regular expressions was removed. + +
+ +In BIDS Validator v1.14.7, the Python validator was rewritten to depend +on the [bidsschematools][] package, and no longer uses the hand-written +regular expressions. At this point, the filename validation of the Python +validator matches that of the Deno (schema) validator. + +#### v1.14.8 + +
+ +```mermaid +graph LR; + subgraph bids-specification; + markdown ---> specification + schema --> bidsschematools --> specification & schema.json + end + subgraph "bids-validator @ v1.14.8"; + regex["filename patterns"] --> Node.js + Node.js --> web/legacy + deno --> web + end + subgraph "python-validator > v1.14.7"; + python + end + + specification -. interpreted .-> regex + schema.json ---> deno + bidsschematools ----> python +``` + +The Python validator was moved into its own repository. +Its versioning and development are no longer tied to the Javascript +validators. + +
+ +After the release of v1.14.7, the Python validator was +removed from the [bids-standard/bids-validator] repository and +relocated to the [bids-standard/python-validator] repository. +Its development, if any takes place, will be independent of +the Javascript validator(s). +Its filename validation will be updated with new releases of [bidsschematools]. + +The legacy validator was moved to . + +#### v2.0 + +
+ +```mermaid +graph LR; + subgraph bids-specification; + markdown ---> specification + schema --> bidsschematools --> specification & schema.json + end + subgraph "legacy-validator @ v1.15.0"; + regex["filename patterns"] --> Node.js + Node.js --> web1["web"] + end + subgraph "bids-validator 2.0+"; + deno --> web + + end + subgraph "python-validator > v1.14.7"; + python + end + + specification -. interpreted .-> regex + schema.json ---> deno + bidsschematools ----> python +``` + +In version 2.0, the Deno validator removed the Node.js +validator from its source tree. + +
+ +For bids-validator 2.0, we have fully separated the Node.js and deno +validators. + +The Node.js validator repository has been renamed to [bids-standard/legacy-validator]. +No further development is planned for this repository. The legacy validator will +continue to be usable at for the +foreseeable future, but it will not receive updates as the standard evolves. + +[bids-standard/bids-validator] will only host the schema-based validator from now on. +We hope that the vast majority of updates will take place in the schema itself, +inside the [bids-standard/bids-specification] repository. + +[bids-standard/python-validator]: https://github.com/bids-standard/python-validator + +[bids-standard/bids-validator]: https://github.com/bids-standard/bids-validator + +[bids-standard/legacy-validator]: https://github.com/bids-standard/legacy-validator + +[bids-standard/bids-specification]: https://github.com/bids-standard/bids-specification + +[bidsschematools]: https://bidsschematools.readthedocs.io/en/latest/ + +[bst desc]: https://bidsschematools.readthedocs.io/en/latest/description.html#organization-and-syntax + +[steering group]: https://bids.neuroimaging.io/governance.html#bids-steering-group + +[checks]: https://github.com/bids-standard/bids-specification/tree/master/src/schema/rules/checks/ + +[deno]: https://deno.com + +[regular expressions]: https://en.wikipedia.org/wiki/Regular_expression + +[py]: https://pypi.org/project/bids-validator/ + +[markdown]: https://en.wikipedia.org/wiki/Markdown + +[flipangle]: https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetic-resonance-imaging-data.html#rf-contrast + +[bids derivatives]: https://bids-specification.readthedocs.io/en/stable/derivatives/introduction.html + +[bids-mrs]: https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetic-resonance-spectroscopy.html + +[npm:validator]: https://www.npmjs.com/package/bids-validator + +[web-validator]: https://bids-validator.readthedocs.io/en/latest/user_guide/web.html + +[command-line]: https://bids-validator.readthedocs.io/en/latest/user_guide/command-line.html + +[validation model]: https://bids-validator.readthedocs.io/en/latest/validation-model/index.html + +[v1.10.0]: https://bids-specification.readthedocs.io/en/v1.10.0/ + +[inheritance principle]: https://bids-specification.readthedocs.io/en/latest/common-principles.html#the-inheritance-principle From d131b5e5886991d8f669c70d314d6e6f520b54ee Mon Sep 17 00:00:00 2001 From: Rockets2theMoon Date: Thu, 14 Nov 2024 09:18:24 -0800 Subject: [PATCH 4/7] updating BIDS impact page (#550) Co-authored-by: Remi Gau Co-authored-by: christinerogers --- docs/impact/index.md | 178 ++++++++++++++++++++++++++++--------------- 1 file changed, 116 insertions(+), 62 deletions(-) diff --git a/docs/impact/index.md b/docs/impact/index.md index f3efe5c1..d4fbe5e3 100644 --- a/docs/impact/index.md +++ b/docs/impact/index.md @@ -1,48 +1,46 @@ -# Impact +# BIDS Impact + +The Brain Imaging Data Structure (BIDS) is an open global community driving the +standardization of neuroscience data across a broad and growing range of modalities +and health research disciplines. First released in June 2016, it is supported by a +worldwide research network and endorsed by organizations like the International +Neuroinformatics Coordinating Facility ([INCF](https://www.incf.org/)). + +BIDS encompasses: + +- Over 40 domain-specific and modality-specific technical specifications across +scientific and technical domains. +- 100+ sample data models for BIDS specifications in +[bids-examples](https://github.com/bids-standard/bids-examples). Read more about +the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/). +- 2000 open datasets across repositories including +[OpenNeuro](https://www.openneuro.org). Read more about [BIDS Datasets](/docs/datasets/index.md). +- Open software conversion and analytics tools, and global infrastructure for +collaborating on emerging standards in neuroscience +[Poldrack, et al, 2024](https://direct.mit.edu/imag/article/doi/10.1162/imag_a_00103/119672/The-past-present-and-future-of-the-brain-imaging). +- ~30,000 annual website visits from a very large community of neuroscience researchers +actively consulting the BIDS specifications (April 2023-24). +- Over 300 BIDS contributors currently supporting and maintaining BIDS community +resources and tools. +- Open working processes through online collaborative tools including GitHub, +GitHub Pages, ReadTheDocs, Google Docs, and OSF. + +The BIDS core steering and maintainers groups work with the community to optimize open +adherence to FAIR principles (Findable, Accessible, Interoperable, and Reusable, +[Wilkinson, et al, 2016](https://www.nature.com/articles/sdata201618)) and to actively +lower barriers to adoption. -This document intends to convey how the BIDS Steering and Maintainers Group can -support your proposed BIDS grant. In an effort to express the impact of BIDS in -the brain imaging community, we have shared several of our traffic metrics. - -## How the BIDS team can help you - -If you are in the process of putting together a grant, **please email/message -the pillar lead** that is most closely associated with your proposed grant so we -may help support this. Our organization is structured into 3 pillars: standard, -tools, and collaboration. - -The respective leads are: - -- Stefan Appelhoff ([stefan.appelhoff@mailbox.org](mailto:stefan.appelhoff@mailbox.org)), -- Chris Markiewicz ([markiewicz@stanford.edu](mailto:markiewicz@stanford.edu)) - -Our range of support covers activities such as: meeting with the Steering and -Maintainers Groups to assisting with connecting you with other BIDS grant -writers or related initiatives to receiving a letter of support from the -Steering Group. - -Regarding **requesting a letter of support** - please submit a drafted letter of -support to the collaboration lead (???) so we may review internally. - -Please include how you plan on giving back to the BIDS community. The primary -mechanism is to support a member of your team to become a BIDS Maintainer. -Letters of support are approved by the Steering Group. This process may take 2-4 -weeks to complete. - -We kindly ask you to please **share your grant online** - successful or not. -This will signal to the rest of the community what avenues we have pursued and -what our fellow colleagues are planning on doing next. These can be grants that -directly extend our support into a new domain, grants that help BIDS (for example -OpenNeuro), or unsuccessful grant applications. - -For example, please find our [NIH-R24 Brain Initiative BIDS-Derivatives grant](https://osf.io/c3dgx/). - -A listing of the previous grants can be found [here](../collaboration/acknowledgments.md) - -## dashboards +## Measuring BIDS Impact ### Datasets +Over the years, the number of shared datasets available to the public has +greatly increased. At its heart, adoption of the BIDS standard across datasets +aids in the sharing of data and collaboration of research through the standardization +of descriptive files names and the organization of data. BIDS organized datasets are +available through public repositories such as [Openneuro.org](https://openneuro.org/) +and the number of publicly available BIDS datasets continues to grow every year. + @@ -51,9 +49,10 @@ https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets- ### Citation Count -BIDS references are centralized in a [zotero group](https://www.zotero.org/groups/5111637/bids) - -You can also find them [in the specification](https://bids-specification.readthedocs.io/en/latest/introduction.html#citing-bids) +As the adoption of the BIDS standard across neuroimaging datasets has grown, so have +citations for work that uses BIDS data and BIDS apps. To aid in searching for publications +relevant to the BIDS standard, we have included some examples of BIDS references that are +centralized in a [zotero group](https://www.zotero.org/groups/5111637/bids) @@ -215,6 +231,44 @@ As of July 1, 2020, we have 183 people signed up for our [BIDS email list](https://forms.gle/JFo2aEkYbKY4EbmE6) and 412 members on our [google group](https://groups.google.com/forum/#!forum/bids-discussion). + +## How the BIDS team can help you + +If you are in the process of putting together a grant, **please email/message +the pillar lead** that is most closely associated with your proposed grant or the +BIDS maintainers email ([bids.maintenance@gmail.com](mailto:bids.maintenance@gmail.com)) +so we may help support this. Our organization is structured into 3 pillars: standard, +tools, and collaboration. + +Our range of support covers activities such as: meeting with the Steering and +Maintainers Groups to assisting with connecting you with other BIDS grant +writers or related initiatives to receiving a letter of support from the +Steering Group. + +Regarding **requesting a letter of support** - please submit a drafted letter of +support to the collaboration lead or the BIDS maintainers email +([bids.maintenance@gmail.com](mailto:bids.maintenance@gmail.com)) so we may review internally. + +Please include how you plan on giving back to the BIDS community. The primary +mechanism is to support a member of your team to become a BIDS Maintainer. +Letters of support are approved by the Steering Group. This process may take 2-4 +weeks to complete. + +We kindly ask you to please **share your grant online** - successful or not. +This will signal to the rest of the community what avenues we have pursued and +what our fellow colleagues are planning on doing next. These can be grants that +directly extend our support into a new domain, grants that help BIDS (for example +OpenNeuro), or unsuccessful grant applications. + +For example, please find our [NIH-R24 Brain Initiative BIDS-Derivatives grant](https://osf.io/c3dgx/). + +A listing of the previous grants can be found [here](../collaboration/acknowledgments.md) + +## Citing BIDS in your project +You can find information on citing BIDS standards for specific modalities and +citing BIDS in general +[in the specification](https://bids-specification.readthedocs.io/en/latest/introduction.html#citing-bids) +