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bids_dataset_info.jbids
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"README.md":"[](https://github.com/bids-standard/bids-examples/actions)\n\n# bids-examples\n\nThis repository contains a set of\n[BIDS-compatible](https://bids.neuroimaging.io/) datasets with **empty raw data\nfiles**. These datasets can be useful to:\n\n1. write lightweight software tests\n1. serve as an example on how a BIDS dataset can be structured\n\n**ALL RAW DATA FILES IN THIS REPOSITORY ARE EMPTY!**\n\nHowever for some of the data, the headers containing the metadata are still\nintact. (For example the NIfTI headers for `.nii` files, the BrainVision data\nheaders for `.vhdr` files, or the OME-XML headers for `.ome.tif` files.)\n\nHeaders are intact for the following datasets:\n\n- `synthetic`\n- Most EEG or iEEG data in BrainVision format (e.g., `eeg_matchingpennies`)\n\n## Validating BIDS examples\n\nThe next three sections mention a few details on how the `bids-examples` can be\nvalidated using `bids-validator`.\n\nFor general information on the `bids-validator`, including installation and\nusage, see the\n[bids-validator README file](https://github.com/bids-standard/bids-validator#quickstart).\n\n### Validating individual examples\n\nSince all raw data files in this repository are empty, the `bids-validator` must\nto be configured to not report empty data files as errors. (See more on\nbids-validator configuration in the\n[bids-validator README](https://github.com/bids-standard/bids-validator#configuration).)\n\nJust run the validator as follows (using the `eeg_matchingpennies` dataset as an\nexample, and assuming you are in a command line at the root of the\n`bids-examples` repository):\n\n`bids-validator eeg_matchingpennies --config.ignore=99`\n\nThe `--config.ignore=99` \"flag\" tells the bids-validator to ignore empty data\nfiles rather than to report the \"empty file\" error .\n\nFor datasets that contain NIfTI `.nii` files, you also need to add the\n`ignoreNiftiHeaders` flag to the `bids-validator` call, to suppress the issue\nthat NIfTI headers are not found.\n\nFor example:\n\n`bids-validator ds003 --config.ignore=99 --ignoreNiftiHeaders`\n\n### Validating all examples\n\nIf you want to validate all examples in one go, you can use the `run_tests.sh`\nscript that is provided in this repository. This script makes use of the\n`bidsconfig.json` configuration file for the `bids-validator`, and appropriately\nhandles some special case examples (see\n[Validator Exceptions](#validator-exceptions)).\n\nSimply run `bash run_tests.sh` in a command line from the root of the\n`bids-examples` repository.\n\n### Validator exceptions\n\nSome datasets may include a custom `.bids-validator-config.json` to ignore\nerrors generated from idiosyncracies of the datasets as they existed on\ncreation.\n\n| name | errors ignored |\n| ------------- | ------------------------------------------------------------------------------------------------------------------------------ |\n| genetics_ukbb | SliceTiming values for tasks is larger than given TR, EchoTime1 and EchoTime2 are not provided for any of the phasediff files. |\n\nOther datasets may include a `.SKIP_VALIDATION` file, to skip the validation\nwith the continuous integration service. This is useful for datasets that\n_cannot_ pass at the moment due to lack of coverage in the\n[bids-validator](https://github.com/bids-standard/bids-validator).\n\nNote however, that the `.SKIP_VALIDATION` file only impacts the continuous\nintegration service, or validation when run with the `run_tests.sh` script (see\n[Validating all examples](#validating-all-examples)). This file does **not**\nhave any effect when running `bids-validator` from custom scripts, the web-based\nvalidator, docker, or from the command line.\n\n| name | why skipped |\n| ----------------- | ------------------------------------------------------ |\n| ds000001-fmriprep | lack of coverage for \"derivatives\" in `bids-validator` |\n\n## Contributing\n\nWe are happy to receive contributions in the form of:\n\n- updates to existing examples, or the [dataset index](dataset-index)\n- new examples\n - only if they cover aspects that are currently not covered by existing\n examples\n - only if a maintainer can be found for this dataset\n- suggestions on how to improve the bids-examples repository\n\nFor more information, please see our\n[CONTRIBUTING.md](https://github.com/bids-standard/bids-examples/blob/master/CONTRIBUTING.md)\nfile or open a\n[new GitHub Issue](https://github.com/bids-standard/bids-examples/issues/new)\nand ask us directly.\n\n## Dataset index\n\nBelow you find several tables with information about the datasets available in\nbids-examples (in alphabetical order).\n\n- [bids-examples](#bids-examples)\n - [Validating BIDS examples](#validating-bids-examples)\n - [Validating individual examples](#validating-individual-examples)\n - [Validating all examples](#validating-all-examples)\n - [Validator exceptions](#validator-exceptions)\n - [Contributing](#contributing)\n - [Dataset index](#dataset-index)\n - [EEG datasets](#eeg-datasets)\n - [iEEG datasets](#ieeg-datasets)\n - [MRI datasets](#mri-datasets)\n - [ASL datasets](#asl-datasets)\n - [qMRI datasets](#qmri-datasets)\n - [PET datasets](#pet-datasets)\n - [Microscopy datasets](#microscopy-datasets)\n - [Motion datasets](#motion-datasets) \n - [NIRS datasets](#nirs-datasets)\n - [Multimodal datasets](#multimodal-datasets)\n\n### EEG datasets\n\n| name | maintained by | description | link to full data |\n| ----------------------------- | ------------- | ------------------------------------------------------------------------------------------------------------------ | --------------------------------------- |\n| eeg_matchingpennies | @sappelhoff | Offline data of BCI experiment decoding left vs. right hand movement. BrainVision data format (.eeg, .vhdr, .vmrk) | https://doi.org/10.17605/OSF.IO/CJ2DR |\n| eeg_rishikesh | @arnodelorme | Mind wandering experiment. EEG data in Biosemi (.bdf) format | https://openneuro.org/datasets/ds001787 |\n| eeg_face13 | @andesha | Deconstructing the early visual electrocortical response to face and house stimuli. EDF format | |\n| eeg_ds003645s_hed | @VisLab | Shows usage of Hierarchical Event Descriptor (HED) in events files | https://openneuro.org/datasets/ds003645 |\n| eeg_ds003645s_hed_inheritance | @VisLab | HED annotation with multiple inherited sidecars | https://openneuro.org/datasets/ds003645 |\n| eeg_ds003645s_hed_longform | @VisLab | HED annotation using tags in long form. | https://openneuro.org/datasets/ds003645 |\n| eeg_ds003645s_hed_library | @VisLab | HED annotation using HED library vocabularies (schema). | https://openneuro.org/datasets/ds003645 |\n| eeg_cbm | @cpernet | Rest EEG. European Data Format (.edf) | |\n\n### iEEG datasets\n\n| name | maintained by | description | link to full data |\n| -------------------- | ------------- | ---------------------------------------------------------------- | ----------------- |\n| ieeg_filtered_speech | @choldgraf | recordings of three seizures | |\n| ieeg_motorMiller2007 | @dorahermes | Cue-based hand & tongue movement data | |\n| ieeg_visual | @dorahermes | Stimulus dependence of gamma oscillations in human visual cortex | |\n\n### MRI datasets\n\n| name | maintained by | description | func | anat | other | link to link to full data |\n| ----------------- | ----------------- | ------------------------------------------------------- | ------------ | ------------------------- | ---------------------- | ------------------------------------------------------ |\n| 7t_trt | | | bold, physio | T1w, quantitative T1 maps | fmap | https://bit.ly/2H0Z6Qt |\n| ds001 | | single task, multiple runs | bold, events | T1w, in-plane T2 | | https://openneuro.org/datasets/ds000001/versions/00006 |\n| ds002 | | multiple tasks, multiple runs | bold, events | T1w, in-plane T2 | | https://openneuro.org/datasets/ds000002/versions/00002 |\n| ds003 | | single task, single run | bold, events | T1w, in-plane T2 | | https://openneuro.org/datasets/ds000003/versions/00001 |\n| ds005 | | single task, multiple runs | bold, events | T1w, in-plane T2 | | https://openneuro.org/datasets/ds000005/versions/00001 |\n| ds006 | | single task, multiple sessions, multiple runs | bold, events | T1w, in-plane T2 | | https://openneuro.org/datasets/ds000006/versions/00001 |\n| ds007 | | single task, multiple runs | bold, events | T1w, in-plane T2 | | https://openneuro.org/datasets/ds000007/versions/00001 |\n| ds008 | | multiple tasks, multiple runs | bold, events | T1w, in-plane T2 | | https://openneuro.org/datasets/ds000008/versions/00001 |\n| ds009 | | multiple tasks, multiple runs | bold, events | T1w, in-plane T2 | | https://openneuro.org/datasets/ds000009/versions/00002 |\n| ds011 | | multiple tasks, multiple runs | bold | T1w | | https://openneuro.org/datasets/ds000011/versions/00001 |\n| ds051 | | multiple tasks, multiple runs | bold | T1w, in-plane T2 | | https://openneuro.org/datasets/ds000051/versions/00001 |\n| ds052 | | multiple tasks, multiple runs | bold | T1w, in-plane T2 | | https://openneuro.org/datasets/ds000052/versions/00001 |\n| ds101 | | single task, multiple runs | bold | T1w | | https://openneuro.org/datasets/ds000101/versions/00004 |\n| ds102 | | single task, multiple runs | bold | T1w | | https://openneuro.org/datasets/ds000102/versions/00001 |\n| ds105 | | single task, multiple runs | bold | T1w | | https://openneuro.org/datasets/ds000105/versions/00001 |\n| ds107 | | single task, multiple runs | bold | T1w | | https://openneuro.org/datasets/ds000107/versions/00001 |\n| ds108 | | single task, multiple runs | bold | T1w | | https://openneuro.org/datasets/ds000108/versions/00002 |\n| ds109 | | multiple tasks, multiple runs | bold | T1w | | https://openneuro.org/datasets/ds000109/versions/00001 |\n| ds110 | | single task, multiple runs | bold | T1w, in-plane T2 | | https://openneuro.org/datasets/ds000110/versions/00001 |\n| ds113b | | forrest gump watching, multiple sessions, multiple runs | bold | T1w, T2w | angiography, dwi, fmap | https://openneuro.org/datasets/ds000113/versions/1.3.0 |\n| ds114 | | multiple tasks, multiple runs | bold | T1w | DWI | https://openneuro.org/datasets/ds000114/versions/1.0.1 |\n| ds116 | | multiple tasks, multiple runs | bold | T1w, in-plane T2 | | https://openneuro.org/datasets/ds000116/versions/00003 |\n| ds210 | | multiple tasks, multiple runs | bold | T1w | | https://openneuro.org/datasets/ds000210/versions/00002 |\n| hcp_example_bids | @robertoostenveld | | bold | T1w | | https://bit.ly/2H0Z6Qt |\n| synthetic | @effigies | A synthetic dataset | bold | T1w | | |\n| ds000001-fmriprep | @effigies | Common derivatives example | bold | T1w | | https://openneuro.org/datasets/ds000001/versions/1.0.0 |\n| ds004332 | @Remi-Gau | Anat dataset with task entity | | FLAIR, T1w, T2starw, T2w | | https://openneuro.org/datasets/ds004332/versions/1.0.2 |\n\n\n### ASL datasets\n\n| name | maintained by | description | link to link to full data |\n| ------ | ------------- | --------------------------------------------------------------------------------------------- | ------------------------- |\n| asl001 | @patsycle | T1w, asl (GE, PCASL, 3D_SPIRAL), m0scan within timeseries | https://osf.io/yru2q/ |\n| asl002 | @patsycle | T1w, asl (Philips, PCASL, 2D_EPI), m0scan as separate scan | https://osf.io/yru2q/ |\n| asl003 | @patsycle | T1w, asl (Siemens, PASL, multiTI), M0scan as separate scan | https://osf.io/yru2q/ |\n| asl004 | @patsycle | T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar appraoch | https://osf.io/yru2q/ |\n| asl005 | @patsycle | T1w, asl (Siemens, PCASL, singleTI, 3D_GRASE), m0scan as separate scan | https://osf.io/yru2q/ |\n\n### qMRI datasets\n\n| name | maintained by | description | link to link to full data |\n| -------------- | ------------------- | ---------------------------------------------------------------------------------------- | ------------------------- |\n| qmri_mp2rage | @Gilles86 | MP2RAGE for T1 mapping | https://osf.io/k4bs5/ |\n| qmri_mp2rageme | @Gilles86 | Multi-echo MP2RAGE | https://osf.io/k4bs5/ |\n| qmri_mpm | @ChristophePhillips | Multi-parametric mapping for R1, R2star, MTsat and PD mapping | https://osf.io/k4bs5/ |\n| qmri_mtsat | @agahkarakuzu | Example dataset for T1 and MTsat mapping. Includes a double-angle B1+ mapping example. | https://osf.io/k4bs5/ |\n| qmri_qsm | @agahkarakuzu | Chimap using fast QSM | `not publicly availabe` |\n| qmri_sa2rage | @agahkarakuzu | Fast B1+ mapping using SA2RAGE | `not publicly availabe` |\n| qmri_vfa | @agahkarakuzu | Variable Flip Angle T1 mapping. Includes an Actual Flip Angle (AFI) B1+ mapping example. | https://osf.io/k4bs5/ |\n| qmri_irt1 | @agahkarakuzu | Inversion Recovery T1 mapping | `not publicly availabe` |\n| qmri_mese | @agahkarakuzu | Multi-Echo Spin-Echo for T2 or Myelin Water Fraction (MWF) mapping. | `not publicly availabe` |\n| qmri_megre | @agahkarakuzu | Multi-Echo Gradient-Echo for T2star mapping. | `not publicly availabe` |\n| qmri_tb1tfl | @agahkarakuzu | B1+ mapping with TurboFLASH readout. | `not publicly availabe` |\n\n### PET datasets\n\n| name | maintained by | description | link to full data |\n| ------ | ------------- | --------------- | ---------------------------------------- |\n| pet001 | @mnoergaard | T1w, PET, blood | |\n| pet002 | @mnoergaard | T1w, PET | https://openneuro.org/datasets/ds001420/ |\n| pet003 | @mnoergaard | T1w, PET, blood | |\n| pet004 | @mnoergaard | PET, blood | |\n| pet005 | @mnoergaard | T1w, PET | |\n\n### Microscopy datasets\n\n| name | maintained by | description | link to full data |\n| ------------- | ------------- | ----------------------------------------------------------------------------------------------- | -------------------------------------- |\n| micr_SEM | @jcohenadad | Example SEM dataset in PNG format with 1 sample imaged over 2 sessions | https://doi.org/10.5281/zenodo.5498378 |\n| micr_SEMzarr | @TheChymera | Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions | |\n| micr_SPIM | @jcohenadad | Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each | https://doi.org/10.5281/zenodo.5517223 |\n\n\n### NIRS datasets\n\n| name | maintained by | description | link to full data |\n| ----------------- | ----------------- | ----------------------------------------------------------------------- | --------------------------------------- |\n| fnirs_tapping | @rob_luke | Example fNIRS measurement with three conditions from five subjects | https://doi.org/10.5281/zenodo.5529797 |\n| fnirs_automaticiy | @robertoostenveld | 24 subjects performing (non-)automatic finger tapping and foot stepping | https://doi.org/10.34973/vesb-mh30 |\n\n\n### Motion datasets\n\n| name | maintained by | description | link to full data |\n| ------------------------ | ------------- | --------------------------------------------------------------------------------------------------------- | ----------------------------------------------- |\n| motion_systemvalidation | @JuliusWelzel | Example dataset of two different motion captured system recorded almost simultaneously, but no brain data | https://doi.org/10.6084/m9.figshare.20238006.v2 |\n\n\n### Multimodal datasets\n\n| name | maintained by | description | mri | meg | eeg | ieeg | genetics | motion | link to full data |\n| ---------------------- | ----------------- | ------------------------------------------------------------------------------------------------------------------------------------ | --------------------- | --- | --- | ---- | -------- | ------ | ------------------------------------------------------------------- |\n| ds000117 | @RikHenson | A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task | anat, dwi, func, fmap | meg | eeg | | | | https://openneuro.org/datasets/ds000117/ |\n| ds000246 | @guiomar | Auditory dataset used for Brainstorm’s general online tutorial | anat | meg | | | | | https://openneuro.org/datasets/ds000246/versions/00001 |\n| ds000247 | @guiomar | Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA). | anat | meg | | | | | https://openneuro.org/datasets/ds000247/versions/00001 |\n| ds000248 | @agramfort | MNE sample data: Data with visual and auditory stimuli | anat | meg | | | | | https://openneuro.org/datasets/ds000248/versions/00001 |\n| eeg_ds000117 | @robertoostenveld | Multimodal (fMRI, MEG, EEG) stripped down to EEG with MRI anatomical scan and electrode coordinates. EEGLAB data format (.set, .fdt) | anat | | eeg | | | | https://openneuro.org/datasets/ds000117/ |\n| eeg_rest_fmri | @cpernet | Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk) | anat, dwi, func | | eeg | | | | |\n| ieeg_epilepsy | @ftadel | multiple sessions, tutorial | anat | | | ieeg | | | https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap_bids |\n| ieeg_epilepsyNWB | @TheChymera | multiple sessions, tutorial — derivative dataset of `ieeg_epilepsy` showcasing the NWB file format alternative | anat | | | ieeg | | | https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap_bids |\n| ieeg_epilepsy_ecog | @ftadel | multiple sessions, tutorial | anat | | | ieeg | | | https://neuroimage.usc.edu/bst/getupdate.php?s=sample_ecog |\n| ieeg_visual_multimodal | @irisgroen | | anat, fmap, func | | | ieeg | | | |\n| genetics_ukbb | @cpernet | multiple tasks, T1w, DTI, BOLD, genetic info | anat, dwi, func, fmap | | | | genetics | | |\n| motion_dualtask | @sjeung | older and younger participants walking while performing discrimination task | | | eeg | | | motion | |\n| motion_spotrotation | @sjeung | participants rotated heading using full-body motion or joystick | | | eeg | | | motion | https://openneuro.org/datasets/ds004460 |\n",
"bidsconfig.json":{
"ignore":99
}
}