From 4713a0a116c9aeee411aca36750ab55b8ca9ad2c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Boris=20Cl=C3=A9net?= Date: Thu, 16 Jan 2025 16:07:51 +0100 Subject: [PATCH 1/7] First version of the hirni-demo --- hcp_example_bids/dataset_description.json | 11 ++- hirni-demo/dataset_description.json | 5 ++ hirni-demo/prov/hirni-demo.prov.jsonld | 90 +++++++++++++++++++ hirni-demo/sourcedata/hirni-demo | 1 + .../anat/sub-02_ses-20130717141500_T1w.json | 23 +++++ .../anat/sub-02_ses-20130717141500_T1w.nii | 0 ...0140425155335_task-oneback_run-1_bold.json | 60 +++++++++++++ ...20140425155335_task-oneback_run-1_bold.nii | 0 8 files changed, 187 insertions(+), 3 deletions(-) create mode 100644 hirni-demo/dataset_description.json create mode 100644 hirni-demo/prov/hirni-demo.prov.jsonld create mode 160000 hirni-demo/sourcedata/hirni-demo create mode 100644 hirni-demo/sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json create mode 100644 hirni-demo/sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii create mode 100644 hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json create mode 100644 hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii diff --git a/hcp_example_bids/dataset_description.json b/hcp_example_bids/dataset_description.json index 842ff92b2..82aaf3395 100644 --- a/hcp_example_bids/dataset_description.json +++ b/hcp_example_bids/dataset_description.json @@ -1,5 +1,10 @@ { - "Name": "Human Connectome Project", - "BIDSVersion": "1.0.2", - "License": "Custom" + "Name": "BIDS-Prov example based on hirni-demo", + "BIDSVersion": "1.10.0", + "SourceDatasets": [ + { + "URL": "https://github.com/psychoinformatics-de/hirni-demo", + "Version": "Commit f5aa766d900037d97c82329e7dfc94ee80086b92" + } + ] } diff --git a/hirni-demo/dataset_description.json b/hirni-demo/dataset_description.json new file mode 100644 index 000000000..842ff92b2 --- /dev/null +++ b/hirni-demo/dataset_description.json @@ -0,0 +1,5 @@ +{ + "Name": "Human Connectome Project", + "BIDSVersion": "1.0.2", + "License": "Custom" +} diff --git a/hirni-demo/prov/hirni-demo.prov.jsonld b/hirni-demo/prov/hirni-demo.prov.jsonld new file mode 100644 index 000000000..8df8af16e --- /dev/null +++ b/hirni-demo/prov/hirni-demo.prov.jsonld @@ -0,0 +1,90 @@ +{ +"@context": "https://purl.org/nidash/bidsprov/context.json", + "BIDSProvVersion": "0.0.1", + "Records": { + "Environments": [ + { + "Id": "urn:fedora", + "Label": "Fedora release 36 (Thirty Six)", + "OperatingSystem": " GNU/Linux 6.2.15-100.fc36.x86_64" + } + ], + "Software": [ + { + "Id": "urn:dcm2niix-4a586b50", + "Label": "dcm2niix", + "Version": "v1.0.20220720" + } + ], + "Activities": [ + { + "Id": "urn:conversion-00f3a18f", + "Label": "Conversion", + "Command": "dcm2niix -o . -f sub-%i/ses-%t/anat/sub-%i_ses-%t_T1w sourcedata/acq1/dicoms/example-dicom-structural-master/dicoms/", + "AssociatedWith": "urn:dcm2niix-4a586b50", + "Used": [ + "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm", + "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm", + "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm" + ] + }, + { + "Id": "urn:conversion-5a66f5be", + "Label": "Conversion", + "Command": "dcm2niix -o . -f sub-%i/ses-%t/func/sub-%i_ses-%t_task-oneback_run-1_bold sourcedata/acq1/dicoms/example-dicom-structural-master/dicoms/", + "AssociatedWith": "urn:dcm2niix-4a586b50", + "Used": [ + "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586", + "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588", + "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590" + ] + } + ], + "Entities": [ + { + "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm", + "Label": "N2D_0001.dcm" + }, + { + "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm", + "Label": "N2D_0002.dcm" + }, + { + "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm", + "Label": "N2D_0003.dcm" + }, + { + "Id": "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586", + "Label": "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586" + }, + { + "Id": "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588", + "Label": "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588" + }, + { + "Id": "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590", + "Label": "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590" + }, + { + "Id": "bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii", + "Label": "sub-02_ses-20130717141500_T1w.nii", + "GeneratedBy": "urn:conversion-00f3a18f" + }, + { + "Id": "bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json", + "Label": "sub-02_ses-20130717141500_T1w.json", + "GeneratedBy": "urn:conversion-00f3a18f" + }, + { + "Id": "bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii", + "Label": "sub-02_ses-20140425155335_task-oneback_run-1_bold.nii", + "GeneratedBy": "urn:conversion-5a66f5be" + }, + { + "Id": "bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json", + "Label": "sub-02_ses-20140425155335_task-oneback_run-1_bold.json", + "GeneratedBy": "urn:conversion-5a66f5be" + }, + ] + } +} \ No newline at end of file diff --git a/hirni-demo/sourcedata/hirni-demo b/hirni-demo/sourcedata/hirni-demo new file mode 160000 index 000000000..f5aa766d9 --- /dev/null +++ b/hirni-demo/sourcedata/hirni-demo @@ -0,0 +1 @@ +Subproject commit f5aa766d900037d97c82329e7dfc94ee80086b92 diff --git a/hirni-demo/sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json b/hirni-demo/sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json new file mode 100644 index 000000000..f8cdff3b6 --- /dev/null +++ b/hirni-demo/sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json @@ -0,0 +1,23 @@ +{ + "Modality": "MR", + "ManufacturersModelName": "nifti2dicom", + "SoftwareVersions": "0.4.11", + "SeriesDescription": "anat-T1w", + "ProtocolName": "anat-T1w", + "ImageType": ["DERIVED", "SECONDARY"], + "RawImage": false, + "SeriesNumber": 401, + "AcquisitionTime": "13:25:18.000000", + "AcquisitionNumber": 1, + "SliceThickness": 0.666667, + "SpacingBetweenSlices": 0.666667, + "ImageOrientationPatientDICOM": [ + 0.999032, + -0.0217884, + 0.0382096, + 0.0265195, + 0.991414, + -0.128044 ], + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220720" +} diff --git a/hirni-demo/sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii b/hirni-demo/sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii new file mode 100644 index 000000000..e69de29bb diff --git a/hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json b/hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json new file mode 100644 index 000000000..17845dd12 --- /dev/null +++ b/hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json @@ -0,0 +1,60 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.753, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva dStream", + "PatientPosition": "HFS", + "ProcedureStepDescription": "Transrep2", + "SoftwareVersions": "5.1.1\\5.1.1.0", + "MRAcquisitionType": "2D", + "SeriesDescription": "func_task-oneback_run-1", + "ProtocolName": "func_task-oneback_run-1", + "ScanningSequence": "GR", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "PulseSequenceName": "FEEPI", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"], + "SeriesNumber": 401, + "AcquisitionTime": "16:04:22.680000", + "AcquisitionNumber": 4, + "PhilipsRWVSlope": 4.00757, + "PhilipsRWVIntercept": 0, + "PhilipsRescaleSlope": 4.00757, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.0132383, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 3, + "SpacingBetweenSlices": 3.3, + "SAR": 0.994626, + "EchoTime": 0.03, + "RepetitionTime": 1.79355, + "RepetitionTimeExcitation": 2, + "MTState": false, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 43, + "PhaseEncodingSteps": 80, + "AcquisitionMatrixPE": 80, + "ReconMatrixPE": 80, + "ParallelReductionFactorInPlane": 2, + "ParallelAcquisitionTechnique": "SENSE", + "WaterFatShift": 12.4991, + "EstimatedEffectiveEchoSpacing": 0.000355975, + "EstimatedTotalReadoutTime": 0.028122, + "AcquisitionDuration": 325.918, + "PixelBandwidth": 1920, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.999805, + -0.0114282, + 0.0161145, + 0.0147905, + 0.973763, + -0.227084 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220720" +} diff --git a/hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii b/hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii new file mode 100644 index 000000000..e69de29bb From 4a33c2e08fcb4e931a72525a6f8585e415ad6d82 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Boris=20Cl=C3=A9net?= Date: Thu, 16 Jan 2025 16:24:46 +0100 Subject: [PATCH 2/7] Adding git modules --- hcp_example_bids/dataset_description.json | 11 +++-------- hirni-demo/.gitmodules | 3 +++ hirni-demo/dataset_description.json | 11 ++++++++--- 3 files changed, 14 insertions(+), 11 deletions(-) create mode 100644 hirni-demo/.gitmodules diff --git a/hcp_example_bids/dataset_description.json b/hcp_example_bids/dataset_description.json index 82aaf3395..842ff92b2 100644 --- a/hcp_example_bids/dataset_description.json +++ b/hcp_example_bids/dataset_description.json @@ -1,10 +1,5 @@ { - "Name": "BIDS-Prov example based on hirni-demo", - "BIDSVersion": "1.10.0", - "SourceDatasets": [ - { - "URL": "https://github.com/psychoinformatics-de/hirni-demo", - "Version": "Commit f5aa766d900037d97c82329e7dfc94ee80086b92" - } - ] + "Name": "Human Connectome Project", + "BIDSVersion": "1.0.2", + "License": "Custom" } diff --git a/hirni-demo/.gitmodules b/hirni-demo/.gitmodules new file mode 100644 index 000000000..3a0e5990a --- /dev/null +++ b/hirni-demo/.gitmodules @@ -0,0 +1,3 @@ +[submodule "sourcedata/hirni-demo"] + path = sourcedata/hirni-demo + url = https://github.com/psychoinformatics-de/hirni-demo.git \ No newline at end of file diff --git a/hirni-demo/dataset_description.json b/hirni-demo/dataset_description.json index 842ff92b2..82aaf3395 100644 --- a/hirni-demo/dataset_description.json +++ b/hirni-demo/dataset_description.json @@ -1,5 +1,10 @@ { - "Name": "Human Connectome Project", - "BIDSVersion": "1.0.2", - "License": "Custom" + "Name": "BIDS-Prov example based on hirni-demo", + "BIDSVersion": "1.10.0", + "SourceDatasets": [ + { + "URL": "https://github.com/psychoinformatics-de/hirni-demo", + "Version": "Commit f5aa766d900037d97c82329e7dfc94ee80086b92" + } + ] } From 6fcbc303aedecf86774268935a4ffed2e54e5339 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Boris=20Cl=C3=A9net?= Date: Thu, 16 Jan 2025 16:36:43 +0100 Subject: [PATCH 3/7] Change gitmodules path --- .gitmodules | 3 +++ hirni-demo/.gitmodules | 3 --- 2 files changed, 3 insertions(+), 3 deletions(-) create mode 100644 .gitmodules delete mode 100644 hirni-demo/.gitmodules diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..38f8c35df --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "hirni-demo/sourcedata/hirni-demo"] + path = hirni-demo/sourcedata/hirni-demo + url = https://github.com/psychoinformatics-de/hirni-demo.git \ No newline at end of file diff --git a/hirni-demo/.gitmodules b/hirni-demo/.gitmodules deleted file mode 100644 index 3a0e5990a..000000000 --- a/hirni-demo/.gitmodules +++ /dev/null @@ -1,3 +0,0 @@ -[submodule "sourcedata/hirni-demo"] - path = sourcedata/hirni-demo - url = https://github.com/psychoinformatics-de/hirni-demo.git \ No newline at end of file From 72aaaedfab63cee6114f967491e28ba858b28d4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Boris=20Cl=C3=A9net?= Date: Fri, 17 Jan 2025 15:48:49 +0100 Subject: [PATCH 4/7] Adding TaskName into bold.json for hirni-demo --- .../func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json | 1 + 1 file changed, 1 insertion(+) diff --git a/hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json b/hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json index 17845dd12..a6bf35c6f 100644 --- a/hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json +++ b/hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json @@ -10,6 +10,7 @@ "MRAcquisitionType": "2D", "SeriesDescription": "func_task-oneback_run-1", "ProtocolName": "func_task-oneback_run-1", + "TaskName": "oneback", "ScanningSequence": "GR", "SequenceVariant": "SK", "ScanOptions": "FS", From cd074e9b374db2f1d7fe097a32bbf2f65272d82a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Boris=20Cl=C3=A9net?= Date: Fri, 17 Jan 2025 16:10:08 +0100 Subject: [PATCH 5/7] Added rich as a missing requirements. Updated dataset listing --- README.md | 61 +++++++++++++++++++++++---------------------- dataset_listing.tsv | 1 + requirements.txt | 3 ++- 3 files changed, 34 insertions(+), 31 deletions(-) diff --git a/README.md b/README.md index e5d4f521c..e3a40e775 100644 --- a/README.md +++ b/README.md @@ -260,36 +260,37 @@ TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. --> -| 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) | +| 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) | +| [hirni-demo](https://github.com/bids-standard/bids-examples/tree/master/hirni-demo) | A BIDS-Prov example showing DICOM to Nifti conversion, based on hirni-demo. (hirni-demo is a demo study dataset for datalad-hirni) | anat, func | T1w, bold | [link](https://github.com/psychoinformatics-de/hirni-demo) | n/a | +| [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 diff --git a/dataset_listing.tsv b/dataset_listing.tsv index 2b0a8afd2..a8ed7470d 100644 --- a/dataset_listing.tsv +++ b/dataset_listing.tsv @@ -82,3 +82,4 @@ mrs_fmrs Functional MRS data involving a pain stimulus task from 15 subjects [li 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 +hirni-demo A BIDS-Prov example showing DICOM to Nifti conversion, based on hirni-demo. (hirni-demo is a demo study dataset for datalad-hirni) https://github.com/psychoinformatics-de/hirni-demo n/a anat, func T1w, bold \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index 51b61b750..8ce76bf7f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,3 +1,4 @@ mkdocs mkdocs-material -pymdown-extensions \ No newline at end of file +pymdown-extensions +rich \ No newline at end of file From 86af27a54e347f24837027a42988c7ad5ae6df94 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Boris=20Cl=C3=A9net?= Date: Fri, 17 Jan 2025 16:19:28 +0100 Subject: [PATCH 6/7] Tab indentation in json sidecar --- .../func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json b/hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json index a6bf35c6f..416ecd35d 100644 --- a/hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json +++ b/hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json @@ -10,7 +10,7 @@ "MRAcquisitionType": "2D", "SeriesDescription": "func_task-oneback_run-1", "ProtocolName": "func_task-oneback_run-1", - "TaskName": "oneback", + "TaskName": "oneback", "ScanningSequence": "GR", "SequenceVariant": "SK", "ScanOptions": "FS", From 1f135806187f028423bd43f8939c0b18d154cda8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Boris=20Cl=C3=A9net?= Date: Tue, 21 Jan 2025 09:31:53 +0100 Subject: [PATCH 7/7] Syntax error in JSON-LD provenance file --- hirni-demo/prov/hirni-demo.prov.jsonld | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/hirni-demo/prov/hirni-demo.prov.jsonld b/hirni-demo/prov/hirni-demo.prov.jsonld index 8df8af16e..99466d5db 100644 --- a/hirni-demo/prov/hirni-demo.prov.jsonld +++ b/hirni-demo/prov/hirni-demo.prov.jsonld @@ -1,5 +1,5 @@ { -"@context": "https://purl.org/nidash/bidsprov/context.json", + "@context": "https://purl.org/nidash/bidsprov/context.json", "BIDSProvVersion": "0.0.1", "Records": { "Environments": [ @@ -84,7 +84,7 @@ "Id": "bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json", "Label": "sub-02_ses-20140425155335_task-oneback_run-1_bold.json", "GeneratedBy": "urn:conversion-5a66f5be" - }, + } ] } } \ No newline at end of file