[DATALAD RUNCMD] Convert subject 02 to BIDS

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "code/containers/scripts/singularity_cmd run code/containers/images/repronim/repronim-reproin--0.9.0.sing -f reproin -s 02 --bids -l '' --minmeta -o . --files inputs/rawdata/dicoms",
 "dsid": "68bdb3f3-eafa-4a48-bddd-31e94e8b8242",
 "exit": 0,
 "extra_inputs": [
  "code/containers/images/repronim/repronim-reproin--0.9.0.sing"
 ],
 "inputs": [
  "inputs/rawdata/dicoms"
 ],
 "outputs": [
  "sub-02"
 ],
 "pwd": "."
}
^^^ Do not change lines above ^^^

.heudiconv/02/info/02.auto.txt

@@ -0,0 +1 @@
+{('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-oneback_run-01_bold', ('nii.gz', 'dicom'), None): ['401-func_task-oneback_run-1']}

.heudiconv/02/info/02.edit.txt

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+{('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-oneback_run-01_bold', ('nii.gz', 'dicom'), None): ['401-func_task-oneback_run-1']}

.heudiconv/02/info/dicominfo.tsv

@@ -0,0 +1,2 @@
+total_files_till_now	example_dcm_file	series_id	dcm_dir_name	series_files	unspecified	dim1	dim2	dim3	dim4	TR	TE	protocol_name	is_motion_corrected	is_derived	patient_id	study_description	referring_physician_name	series_description	sequence_name	image_type	accession_number	patient_age	patient_sex	date	series_uid
+5460	MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586	401-func_task-oneback_run-1	dicoms	5460		80	80	5460	1	2.00000061035156	30.0	func_task-oneback_run-1	False	False	02	Hanke_Stadler^0083_transrep2		func_task-oneback_run-1		('ORIGINAL', 'PRIMARY', 'M_FFE', 'M', 'FFE')		42	F	20140425	1.2.826.0.1.3680043.2.1143.5321353203983731308636763388634496705

CHANGES

@@ -0,0 +1,5 @@
+0.0.1  Initial data acquired
+TODOs:
+	- verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208)
+	- fill out dataset_description.json, README, sourcedata/README (if present)
+	- provide _events.tsv file for each _bold.nii.gz with onsets of events (see  '8.5 Task events'  of BIDS specification)

dataset_description.json

@@ -0,0 +1,23 @@
+{
+  "Acknowledgements": "We thank Terry Sacket and the rest of the DBIC (Dartmouth Brain Imaging Center) personnel for assistance in data collection, and Yaroslav Halchenko and Matteo Visconti for preparing BIDS dataset. TODO: more",
+  "Authors": [
+    "TODO:",
+    "First1 Last1",
+    "First2 Last2",
+    "..."
+  ],
+  "BIDSVersion": "1.4.1",
+  "DatasetDOI": "TODO: eventually a DOI for the dataset",
+  "Funding": [
+    "TODO",
+    "GRANT #1",
+    "GRANT #2"
+  ],
+  "HowToAcknowledge": "TODO: describe how to acknowledge -- either cite a corresponding paper, or just in acknowledgement section",
+  "License": "TODO: choose a license, e.g. PDDL (http://opendatacommons.org/licenses/pddl/)",
+  "Name": "TODO: name of the dataset",
+  "ReferencesAndLinks": [
+    "TODO",
+    "List of papers or websites"
+  ]
+}

participants.json

@@ -0,0 +1,14 @@
+{
+  "participant_id": {
+    "Description": "Participant identifier"
+  },
+  "age": {
+    "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions"
+  },
+  "sex": {
+    "Description": "self-rated by participant, M for male/F for female (TODO: verify)"
+  },
+  "group": {
+    "Description": "(TODO: adjust - by default everyone is in control group)"
+  }
+}

participants.tsv

@@ -0,0 +1,2 @@
+participant_id	age	sex	group
+sub-02	42	F	control

sourcedata/README

@@ -0,0 +1,2 @@
+TODO: Provide description about source data, e.g. 
+Directory below contains DICOMS compressed into tarballs per each sequence, replicating directory hierarchy of the BIDS dataset itself.

sourcedata/sub-02/func/sub-02_task-oneback_run-01_bold.dicom.tgz

@@ -0,0 +1 @@
+../../../.git/annex/objects/j8/1J/MD5E-s25681682--49fb2df7230ebd27b107c490554e01fa.tgz/MD5E-s25681682--49fb2df7230ebd27b107c490554e01fa.tgz

sub-02/func/sub-02_task-oneback_run-01_bold.json

@@ -0,0 +1,57 @@
+{
+  "AcquisitionMatrixPE": 80,
+  "AcquisitionNumber": 4,
+  "AcquisitionTime": "16:04:22.680000",
+  "CoilString": "MULTI COIL",
+  "ConversionSoftware": "dcm2niix",
+  "ConversionSoftwareVersion": "v1.0.20201102",
+  "EchoTime": 0.03,
+  "EchoTrainLength": 43,
+  "EstimatedEffectiveEchoSpacing": 0.000355975,
+  "EstimatedTotalReadoutTime": 0.028122,
+  "FlipAngle": 90,
+  "ImageOrientationPatientDICOM": [0.999805, -0.0114282, 0.0161145, 0.0147905, 0.973763, -0.227084],
+  "ImageType": [
+    "ORIGINAL",
+    "PRIMARY",
+    "M",
+    "FFE",
+    "M",
+    "FFE"
+],
+  "ImagingFrequency": 127.753,
+  "InPlanePhaseEncodingDirectionDICOM": "COL",
+  "MRAcquisitionType": "2D",
+  "MagneticFieldStrength": 3,
+  "Manufacturer": "Philips",
+  "ManufacturersModelName": "Achieva dStream",
+  "Modality": "MR",
+  "ParallelReductionFactorInPlane": 2,
+  "PatientPosition": "HFS",
+  "PercentPhaseFOV": 100,
+  "PercentSampling": 100,
+  "PhaseEncodingAxis": "j",
+  "PhaseEncodingSteps": 80,
+  "PhilipsRWVIntercept": 0,
+  "PhilipsRWVSlope": 4.00757,
+  "PhilipsRescaleIntercept": 0,
+  "PhilipsRescaleSlope": 4.00757,
+  "PhilipsScaleSlope": 0.0132383,
+  "PixelBandwidth": 1920,
+  "ProcedureStepDescription": "Transrep2",
+  "ProtocolName": "func_task-oneback_run-1",
+  "ReconMatrixPE": 80,
+  "RepetitionTime": 1.79355,
+  "RepetitionTimeExcitation": 2,
+  "SAR": 0.994626,
+  "ScanOptions": "FS",
+  "ScanningSequence": "GR",
+  "SequenceVariant": "SK",
+  "SeriesDescription": "func_task-oneback_run-1",
+  "SeriesNumber": 401,
+  "SliceThickness": 3,
+  "SoftwareVersions": "5.1.1\\5.1.1.0",
+  "SpacingBetweenSlices": 3.3,
+  "TaskName": "oneback",
+  "UsePhilipsFloatNotDisplayScaling": 1,
+  "WaterFatShift": 12.4991}

sub-02/func/sub-02_task-oneback_run-01_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/kZ/K5/MD5E-s24180157--aeb0e5f2e2d5fe4ade97117a8cc5232f.nii.gz/MD5E-s24180157--aeb0e5f2e2d5fe4ade97117a8cc5232f.nii.gz

sub-02/func/sub-02_task-oneback_run-01_events.tsv

@@ -0,0 +1 @@
+onset	duration	trial_type	response_time	stim_file	TODO -- fill in rows and add more tab-separated columns if desired

sub-02/sub-02_scans.json

@@ -0,0 +1,16 @@
+{
+  "filename": {
+    "Description": "Name of the nifti file"
+  },
+  "acq_time": {
+    "LongName": "Acquisition time",
+    "Description": "Acquisition time of the particular scan"
+  },
+  "operator": {
+    "Description": "Name of the operator"
+  },
+  "randstr": {
+    "LongName": "Random string",
+    "Description": "md5 hash of UIDs"
+  }
+}

sub-02/sub-02_scans.tsv

@@ -0,0 +1,2 @@
+filename	acq_time	operator	randstr
+func/sub-02_task-oneback_run-01_bold.nii.gz	2014-04-25T16:04:22.680000	n/a	c2b66122

task-oneback_bold.json

@@ -0,0 +1,58 @@
+{
+  "AcquisitionMatrixPE": 80,
+  "AcquisitionNumber": 4,
+  "AcquisitionTime": "16:04:22.680000",
+  "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO",
+  "CoilString": "MULTI COIL",
+  "ConversionSoftware": "dcm2niix",
+  "ConversionSoftwareVersion": "v1.0.20201102",
+  "EchoTime": 0.03,
+  "EchoTrainLength": 43,
+  "EstimatedEffectiveEchoSpacing": 0.000355975,
+  "EstimatedTotalReadoutTime": 0.028122,
+  "FlipAngle": 90,
+  "ImageOrientationPatientDICOM": [0.999805, -0.0114282, 0.0161145, 0.0147905, 0.973763, -0.227084],
+  "ImageType": [
+    "ORIGINAL",
+    "PRIMARY",
+    "M",
+    "FFE",
+    "M",
+    "FFE"
+],
+  "ImagingFrequency": 127.753,
+  "InPlanePhaseEncodingDirectionDICOM": "COL",
+  "MRAcquisitionType": "2D",
+  "MagneticFieldStrength": 3,
+  "Manufacturer": "Philips",
+  "ManufacturersModelName": "Achieva dStream",
+  "Modality": "MR",
+  "ParallelReductionFactorInPlane": 2,
+  "PatientPosition": "HFS",
+  "PercentPhaseFOV": 100,
+  "PercentSampling": 100,
+  "PhaseEncodingAxis": "j",
+  "PhaseEncodingSteps": 80,
+  "PhilipsRWVIntercept": 0,
+  "PhilipsRWVSlope": 4.00757,
+  "PhilipsRescaleIntercept": 0,
+  "PhilipsRescaleSlope": 4.00757,
+  "PhilipsScaleSlope": 0.0132383,
+  "PixelBandwidth": 1920,
+  "ProcedureStepDescription": "Transrep2",
+  "ProtocolName": "func_task-oneback_run-1",
+  "ReconMatrixPE": 80,
+  "RepetitionTime": 1.79355,
+  "RepetitionTimeExcitation": 2,
+  "SAR": 0.994626,
+  "ScanOptions": "FS",
+  "ScanningSequence": "GR",
+  "SequenceVariant": "SK",
+  "SeriesDescription": "func_task-oneback_run-1",
+  "SeriesNumber": 401,
+  "SliceThickness": 3,
+  "SoftwareVersions": "5.1.1\\5.1.1.0",
+  "SpacingBetweenSlices": 3.3,
+  "TaskName": "TODO: full task name for oneback",
+  "UsePhilipsFloatNotDisplayScaling": 1,
+  "WaterFatShift": 12.4991}