Merge branch 'testdata' into surf_csv

test_data/README.md

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+# Test data for HippUnfold
+
+Nearly all the data in this folder are "fake", i.e. zero-sized files, used *only* for dry-run testing.
+
+The only folder here with *actual* nifti images is `ds002168`, which contains a single subject T1w and high-res T2w data.

test_data/ds002168/README.md

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+Excerpt of OpenNeuro ds002168 dataset (anatomical T1w, T2w) used solely as a test case for hippunfold.
+

test_data/ds002168/dataset_description.json

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+{
+    "Name": "Subset of: Pattern Separation beyond the Hippocampus: A High-Resolution Whole-Brain Investigation of Mnemonic Discrimination in Healthy Adults",
+    "Description": "Anatomical data from a single subject used for testing purposes",
+    "BIDSVersion": "1.1.1",
+    "License": "CC0",
+    "Authors": [
+        "Michelle I. Nash",
+        "Cooper B. Hodges",
+        "Nathan M. Muncy",
+        "C. Brock Kirwan"
+    ],
+    "ReferencesAndLinks": [
+        "https://doi.org/10.1002/hipo.23299"
+    ],
+    "DatasetDOI": "10.18112/openneuro.ds002168.v1.1.0"
+}

test_data/ds002168/sub-1425/anat/sub-1425_T1w.json

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+{
+	"Modality": "MR",
+	"MagneticFieldStrength": 3,
+	"Manufacturer": "Siemens",
+	"ManufacturersModelName": "TrioTim",
+	"InstitutionName": "Brigham_Young_University",
+	"InstitutionalDepartmentName": "MRI",
+	"InstitutionAddress": "University_Pkwy_1700_North_685_Provo_UT_US_84601",
+	"DeviceSerialNumber": "35002",
+	"StationName": "MININT-E41B04",
+	"PatientPosition": "HFS",
+	"ProcedureStepDescription": "Research_KIRWAN",
+	"SoftwareVersions": "syngo_MR_B17",
+	"MRAcquisitionType": "3D",
+	"SeriesDescription": "t1_fl3d_sag_no3Daccel_iso_1.0_1avg",
+	"ProtocolName": "t1_fl3d_sag_no3Daccel_iso_1.0_1avg",
+	"ScanningSequence": "GR",
+	"SequenceVariant": "SP",
+	"SequenceName": "_fl3d1_ns",
+	"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"],
+	"SeriesNumber": 9,
+	"AcquisitionTime": "10:00:29.287500",
+	"AcquisitionNumber": 1,
+	"SliceThickness": 1,
+	"SAR": 0.178544,
+	"EchoTime": 0.00492,
+	"RepetitionTime": 0.02,
+	"FlipAngle": 25,
+	"PartialFourier": 1,
+	"BaseResolution": 256,
+	"ShimSetting": [
+		-2655,
+		-23109,
+		2059,
+		81,
+		-13,
+		-145,
+		-152,
+		15	],
+	"TxRefAmp": 338.876,
+	"PhaseResolution": 1,
+	"ReceiveCoilName": "32Ch_Head",
+	"PulseSequenceDetails": "%SiemensSeq%_gre",
+	"PercentPhaseFOV": 100,
+	"PhaseEncodingSteps": 255,
+	"AcquisitionMatrixPE": 256,
+	"ReconMatrixPE": 256,
+	"ParallelReductionFactorInPlane": 2,
+	"PixelBandwidth": 190,
+	"DwellTime": 1.03e-05,
+	"ImageOrientationPatientDICOM": [
+		0.0383878,
+		0.999263,
+		0,
+		0,
+		-1e-16,
+		-1	],
+	"InPlanePhaseEncodingDirectionDICOM": "ROW",
+	"ConversionSoftware": "dcm2niix",
+	"ConversionSoftwareVersion": "v1.0.20180404 Clang8.0.0"
+}

test_data/ds002168/sub-1425/anat/sub-1425_T2w.json

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+{
+	"Modality": "MR",
+	"MagneticFieldStrength": 3,
+	"Manufacturer": "Siemens",
+	"ManufacturersModelName": "TrioTim",
+	"InstitutionName": "Brigham_Young_University",
+	"InstitutionalDepartmentName": "MRI",
+	"InstitutionAddress": "University_Pkwy_1700_North_685_Provo_UT_US_84601",
+	"DeviceSerialNumber": "35002",
+	"StationName": "MININT-E41B04",
+	"PatientPosition": "HFS",
+	"ProcedureStepDescription": "Research_KIRWAN",
+	"SoftwareVersions": "syngo_MR_B17",
+	"MRAcquisitionType": "2D",
+	"SeriesDescription": "HHR_struct_MODIFIED",
+	"ProtocolName": "HHR_struct_MODIFIED",
+	"ScanningSequence": "SE",
+	"SequenceVariant": "SK_SP_OSP",
+	"SequenceName": "_tse2d1_15",
+	"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"],
+	"SeriesNumber": 16,
+	"AcquisitionTime": "10:25:29.757500",
+	"AcquisitionNumber": 1,
+	"SliceThickness": 2,
+	"SpacingBetweenSlices": 2,
+	"SAR": 0.871445,
+	"EchoTime": 0.064,
+	"RepetitionTime": 6,
+	"FlipAngle": 129,
+	"PartialFourier": 1,
+	"BaseResolution": 512,
+	"ShimSetting": [
+		-2642,
+		-23146,
+		2594,
+		1131,
+		68,
+		-545,
+		359,
+		-103	],
+	"TxRefAmp": 338.876,
+	"PhaseResolution": 1,
+	"PhaseOversampling": 0.4,
+	"ReceiveCoilName": "32Ch_Head",
+	"PulseSequenceDetails": "%SiemensSeq%_tse",
+	"PercentPhaseFOV": 100,
+	"EchoTrainLength": 15,
+	"PhaseEncodingSteps": 720,
+	"AcquisitionMatrixPE": 512,
+	"ReconMatrixPE": 512,
+	"PixelBandwidth": 195,
+	"DwellTime": 5e-06,
+	"PhaseEncodingDirection": "i",
+	"ImageOrientationPatientDICOM": [
+		0.99997,
+		0.00779698,
+		-1.51035e-10,
+		-0.00404605,
+		0.518909,
+		-0.85482	],
+	"InPlanePhaseEncodingDirectionDICOM": "ROW",
+	"ConversionSoftware": "dcm2niix",
+	"ConversionSoftwareVersion": "v1.0.20180404 Clang8.0.0"
+}