BIDS-Prov demo using dcm2niix on hirni-demo data

.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

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

hirni-demo/dataset_description.json

@@ -0,0 +1,10 @@
+{
+  "Name": "BIDS-Prov example based on hirni-demo",
+  "BIDSVersion": "1.10.0",
+  "SourceDatasets": [
+    {
+      "URL": "https://github.com/psychoinformatics-de/hirni-demo",
+      "Version": "Commit f5aa766d900037d97c82329e7dfc94ee80086b92"
+    }
+  ]
+}

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"
+      }
+    ]
+  }
+}

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"
+}

hirni-demo/sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json

@@ -0,0 +1,61 @@
+{
+	"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",
+	"TaskName": "oneback",
+	"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"
+}

requirements.txt

@@ -1,3 +1,4 @@
 mkdocs
 mkdocs-material
-pymdown-extensions
+pymdown-extensions
+rich