diff --git a/README.md b/README.md index 8fe5da9f6..e5d4f521c 100644 --- a/README.md +++ b/README.md @@ -136,6 +136,19 @@ DO NOT EDIT DIRECTLY. | [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 | +|:------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------|:--------------------------------|:---------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:-------------------------------------------| +| [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 | +|:------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------|:------------------------------------------------|:---------------------------------------------| +| [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 | 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) | +| 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 @@ -190,13 +231,13 @@ TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. --> -| 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) | -| [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 | photo, samples, sessions | [link](https://human-organ-atlas.esrf.eu/datasets/572252538) | [@chourroutm](https://github.com/chourroutm) | +| 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 @@ -205,12 +246,12 @@ TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. --> -| 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) | +| 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 @@ -257,8 +298,11 @@ TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. --> -| name | description | datatypes | suffixes | link to full data | maintained by | -|--------|---------------|-------------|------------|---------------------|-----------------| +| 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 @@ -307,16 +351,3 @@ DO NOT EDIT DIRECTLY. | [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, 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/dataset_listing.tsv b/dataset_listing.tsv index 7f49cca7c..2b0a8afd2 100644 --- a/dataset_listing.tsv +++ b/dataset_listing.tsv @@ -2,7 +2,7 @@ name description link to full data maintained by datatypes suffixes eeg_matchingpennies Offline data of BCI experiment decoding left vs. right hand movement. BrainVision data format (.eeg, .vhdr, .vmrk) [link](https://doi.org/10.17605/OSF.IO/CJ2DR) [@sappelhoff](https://github.com/sappelhoff) eeg channels, eeg, events eeg_rishikesh Mind wandering experiment. EEG data in Biosemi (.bdf) format [link](https://openneuro.org/datasets/ds001787) [@arnodelorme](https://github.com/arnodelorme) eeg channels, eeg, events eeg_face13 Deconstructing the early visual electrocortical response to face and house stimuli. EDF format [@andesha](https://github.com/andesha) eeg channels, coordsystem, eeg, electrodes, events -eeg_ds003645s_hed_demo Shows usage of Hierarchical Event Descriptor (HED) in .tsv files [link](https://openneuro.org/datasets/ds003645) [@VisLab](https://github.com/VisLab) anat, beh, eeg, micr, motion KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, headshape, motion, photo, samples, scans +eeg_ds003645s_hed_demo Shows usage of Hierarchical Event Descriptor (HED) in .tsv files [link](https://openneuro.org/datasets/ds003645) [@VisLab](https://github.com/VisLab) anat, beh, eeg, micr, motion KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans eeg_ds003645s_hed_library HED annotation using HED library vocabularies (schema). [link](https://openneuro.org/datasets/ds003645) [@VisLab](https://github.com/VisLab) eeg channels, eeg, events eeg_cbm Rest EEG. European Data Format (.edf) [@cpernet](https://github.com/cpernet) eeg channels, eeg, events, scans ieeg_filtered_speech recordings of three seizures [@choldgraf](https://github.com/choldgraf) ieeg channels, coordsystem, electrodes, events, ieeg, photo @@ -59,13 +59,13 @@ pet005 T1w, PET [@mnoergaard](https://github.com/mnoergaard) anat, pet T1w, eve micr_SEM Example SEM dataset in PNG format with 1 sample imaged over 2 sessions [link](https://doi.org/10.5281/zenodo.5498378) [@jcohenadad](https://github.com/jcohenadad) micr SEM, photo, samples, sessions micr_SEMzarr Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions [@TheChymera](https://github.com/TheChymera) micr SEM, SPIM, samples, sessions micr_SPIM Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each [link](https://doi.org/10.5281/zenodo.5517223) [@jcohenadad](https://github.com/jcohenadad) micr SPIM, photo, samples -micr_XPCTzarr Example XPCT dataset in OME-ZARR format with 1 sample imaged [link](https://human-organ-atlas.esrf.eu/datasets/572252538) [@chourroutm](https://github.com/chourroutm) micr photo, samples, sessions +micr_XPCTzarr Example XPCT dataset in OME-ZARR format with 1 sample imaged [link](https://human-organ-atlas.esrf.eu/datasets/572252538) [@chourroutm](https://github.com/chourroutm) micr XPCT, photo, samples, sessions fnirs_tapping Example fNIRS measurement with three conditions from five subjects [link](https://doi.org/10.5281/zenodo.5529797) [@rob-luke](https://github.com/rob-luke) nirs channels, coordsystem, events, nirs, optodes, scans fnirs_automaticity 24 subjects performing (non-)automatic finger tapping and foot stepping [link](https://doi.org/10.34973/vesb-mh30) [@robertoostenveld](https://github.com/robertoostenveld) nirs channels, coordsystem, events, nirs, optodes, practicelogbook, scans motion_systemvalidation Example dataset of two different motion captured system recorded almost simultaneously, but no brain data [link](https://doi.org/10.6084/m9.figshare.20238006.v2) [@JuliusWelzel](https://github.com/JuliusWelzel) motion channels, motion, scans ds000117 A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task [link](https://openneuro.org/datasets/ds000117/) [@RikHenson](https://github.com/RikHenson) anat, beh, dwi, fmap, func, meg FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans -ds000246 Auditory dataset used for Brainstorm’s general online tutorial [link](https://openneuro.org/datasets/ds000246/versions/00001) [@guiomar](https://github.com/guiomar) anat, meg ChannelGroupSet, ClassFile, MarkerFile, T1w, channels, coordsystem, default, headshape, meg, params, photo, processing, scans -ds000247 Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA). [link](https://openneuro.org/datasets/ds000247/versions/00001) [@guiomar](https://github.com/guiomar) anat, meg ClassFile, T1w, bad, channels, coordsystem, default, headshape, meg, params, processing, scans +ds000246 Auditory dataset used for Brainstorm’s general online tutorial [link](https://openneuro.org/datasets/ds000246/versions/00001) [@guiomar](https://github.com/guiomar) anat, meg T1w, channels, coordsystem, headshape, meg, photo, scans +ds000247 Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA). [link](https://openneuro.org/datasets/ds000247/versions/00001) [@guiomar](https://github.com/guiomar) anat, meg T1w, channels, coordsystem, headshape, meg, scans ds000248 MNE sample data: Data with visual and auditory stimuli [link](https://openneuro.org/datasets/ds000248/versions/00001) [@agramfort](https://github.com/agramfort) anat, meg FLASH, T1w, channels, coordsystem, events, meg, scans eeg_ds000117 Multimodal (fMRI, MEG, EEG) stripped down to EEG with MRI anatomical scan and electrode coordinates. EEGLAB data format (.set, .fdt) [link](https://openneuro.org/datasets/ds000117/) [@robertoostenveld](https://github.com/robertoostenveld) anat, eeg T1w, channels, coordsystem, eeg, electrodes, events eeg_rest_fmri Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk) [@cpernet](https://github.com/cpernet) anat, dwi, eeg, func T1w, bold, dwi, eeg @@ -76,9 +76,9 @@ ieeg_visual_multimodal [@irisgroen](https://github.com/irisgroen) anat, fmap, genetics_ukbb multiple tasks, T1w, DTI, BOLD, genetic info [@cpernet](https://github.com/cpernet) anat, dwi, func FLAIR, T1w, bold, dwi, events, info motion_dualtask older and younger participants walking while performing discrimination task [@sjeung](https://github.com/sjeung) eeg, motion channels, eeg, events, motion, scans motion_spotrotation participants rotated heading using full-body motion or joystick [link](https://openneuro.org/datasets/ds004460) [@sjeung](https://github.com/sjeung) eeg, motion channels, coordsystem, eeg, electrodes, events, motion, scans -mrs_2dmrsi 2D sLASER MRSI data from 8 subjects [link](https://zenodo.org/records/7701228) [@markmikkelsen](https://github.com/markmikkelsen) anat T1w -mrs_biggaba MEGA-PRESS and PRESS MRS data from 12 subjects from one site from the Big GABA project [link](https://www.nitrc.org/projects/biggaba) [@markmikkelsen](https://github.com/markmikkelsen) anat T1w -mrs_fmrs Functional MRS data involving a pain stimulus task from 15 subjects [link](https://www.nitrc.org/projects/fmrs_2020) [@markmikkelsen](https://github.com/markmikkelsen) anat T1w, events +mrs_2dmrsi 2D sLASER MRSI data from 8 subjects [link](https://zenodo.org/records/7701228) [@markmikkelsen](https://github.com/markmikkelsen) anat, mrs T1w, mrsi +mrs_biggaba MEGA-PRESS and PRESS MRS data from 12 subjects from one site from the Big GABA project [link](https://www.nitrc.org/projects/biggaba) [@markmikkelsen](https://github.com/markmikkelsen) anat, mrs T1w, mrsref, svs +mrs_fmrs Functional MRS data involving a pain stimulus task from 15 subjects [link](https://www.nitrc.org/projects/fmrs_2020) [@markmikkelsen](https://github.com/markmikkelsen) anat, mrs T1w, events, mrsref, svs 2d_mb_pcasl Siemens 2D MultiBand Multi-delay PCASL (m0 and noRF included within timeseries) [link](https://osf.io/xrkc4/) [@aptinis](https://github.com/aptinis) anat, fmap, perf T1w, asl, aslcontext, epi xeeg_hed_score EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE [@dorahermes](https://github.com/dorahermes) anat, eeg, ieeg T1w, channels, coordsystem, eeg, electrodes, events, ieeg dwi_deriv exemplifies the storage of diffusion MRI derivates that may be generated on the Siemens XA platform. dwi dwi diff --git a/tools/print_dataset_listing.py b/tools/print_dataset_listing.py index 49b7efbb3..18ebd78af 100644 --- a/tools/print_dataset_listing.py +++ b/tools/print_dataset_listing.py @@ -4,10 +4,12 @@ You can pass an argument to insert the content in another file. Otherwise the content will be added to the README of this repository. """ + import sys from pathlib import Path import pandas as pd from bids import BIDSLayout +from rich import print folders_to_skip = ["docs", ".git", ".github", "tools", "env", "site", ".vscode"] suffixes_to_remove = ["README", "description", "participants", "CITATION"] @@ -23,15 +25,18 @@ UPSTREAM_REPO = "https://github.com/bids-standard/bids-examples/tree/master/" # set to True to update the listing of datasets with the datatypes and suffixes -update_content = True +update_content = False root = Path(__file__).resolve().parent.parent input_file = root / "dataset_listing.tsv" tables_order = { "ASL": "perf", + "Behavioral": "beh", "EEG": "^eeg$", + "DWI": "dwi", "iEEG": "ieeg", + "HED": "", "MEG": "meg", "Microscopy": "micr", "Motion": "motion", @@ -40,11 +45,11 @@ "NIRS": "nirs", "PET": "pet", "qMRI": "", - "Behavioral": "beh", } DELIMITER = "" + def main(output_file=None): if len(sys.argv) > 1: @@ -55,6 +60,8 @@ def main(output_file=None): df = pd.read_csv(input_file, sep="\t") + names = df["name"].copy() + check_missing_folders(df, root) if update_content: @@ -64,12 +71,10 @@ def main(output_file=None): df = add_links(df) - print(df) - clean_previous_run(output_file) df = df[column_order] - add_tables(df, output_file) + add_tables(df, output_file, names) def check_missing_folders(df, root): @@ -93,10 +98,12 @@ def update_datatypes_and_suffixes(df, root): layout = BIDSLayout(root / row[1]["name"]) tmp = sorted(layout.get_datatypes()) or ["n/a"] + print(f" {tmp}") datatypes.append(stringify_list(tmp)) tmp = layout.get_suffixes() tmp = sorted([s for s in tmp if s not in suffixes_to_remove]) or ["n/a"] + print(f" {tmp}") suffixes.append(stringify_list(tmp)) if not datatypes: @@ -122,7 +129,6 @@ def add_links(df): return df - def clean_previous_run(output_file: Path) -> None: print("Cleaning output files from previous run...") lines = output_file.read_text().split("\n") @@ -134,28 +140,38 @@ def clean_previous_run(output_file: Path) -> None: break f.write(line + "\n") + def add_warning(f): - f.write(""" -""".upper()) +""".upper() + ) + -def add_tables(df: pd.DataFrame, output_file: Path) -> None: +def add_tables(df: pd.DataFrame, output_file: Path, names) -> None: print("Writing markdown tables...") df.fillna("n/a", inplace=True) for table_name, table_datatypes in tables_order.items(): with output_file.open("a") as f: f.write(f"\n### {table_name}\n\n") add_warning(f) + if table_name == "qMRI": - sub_df = df[df["name"].str.contains("qmri_")] + mask = names.str.contains("qmri_") + elif table_name == "HED": + mask = names.str.contains("_hed_") else: - sub_df = df[df["datatypes"].str.contains(table_datatypes, regex=True)] + mask = df["datatypes"].str.contains(table_datatypes, regex=True) + + sub_df = df[mask].copy() sub_df.sort_values(by=["name"], inplace=True) - # sub_df["name"] = df["name"].apply(lambda x: f'[{x}](https://github.com/bids-standard/bids-examples/tree/master/{x})') + print(sub_df) + sub_df.to_markdown(output_file, index=False, mode="a") with output_file.open("a") as f: f.write("\n")