diff --git a/test_data/README.md b/test_data/README.md new file mode 100644 index 00000000..b1feadf2 --- /dev/null +++ b/test_data/README.md @@ -0,0 +1,5 @@ +# 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. diff --git a/test_data/ds002168/README.md b/test_data/ds002168/README.md new file mode 100644 index 00000000..e8dd2485 --- /dev/null +++ b/test_data/ds002168/README.md @@ -0,0 +1,2 @@ +Excerpt of OpenNeuro ds002168 dataset (anatomical T1w, T2w) used solely as a test case for hippunfold. + diff --git a/test_data/ds002168/dataset_description.json b/test_data/ds002168/dataset_description.json new file mode 100644 index 00000000..49be95e7 --- /dev/null +++ b/test_data/ds002168/dataset_description.json @@ -0,0 +1,16 @@ +{ + "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" +} diff --git a/test_data/ds002168/sub-1425/anat/sub-1425_T1w.json b/test_data/ds002168/sub-1425/anat/sub-1425_T1w.json new file mode 100644 index 00000000..8ccbf9e3 --- /dev/null +++ b/test_data/ds002168/sub-1425/anat/sub-1425_T1w.json @@ -0,0 +1,61 @@ +{ + "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" +} diff --git a/test_data/ds002168/sub-1425/anat/sub-1425_T1w.nii.gz b/test_data/ds002168/sub-1425/anat/sub-1425_T1w.nii.gz new file mode 100644 index 00000000..c2f6b7c1 Binary files /dev/null and b/test_data/ds002168/sub-1425/anat/sub-1425_T1w.nii.gz differ diff --git a/test_data/ds002168/sub-1425/anat/sub-1425_T2w.json b/test_data/ds002168/sub-1425/anat/sub-1425_T2w.json new file mode 100644 index 00000000..0b3b17cd --- /dev/null +++ b/test_data/ds002168/sub-1425/anat/sub-1425_T2w.json @@ -0,0 +1,64 @@ +{ + "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" +} diff --git a/test_data/ds002168/sub-1425/anat/sub-1425_T2w.nii.gz b/test_data/ds002168/sub-1425/anat/sub-1425_T2w.nii.gz new file mode 100644 index 00000000..b8366b4d Binary files /dev/null and b/test_data/ds002168/sub-1425/anat/sub-1425_T2w.nii.gz differ