initial commit

README.md

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+# README
+
+## Content
+
+This contains an high-res (0.7 mm) MP2RAGE of yours truly.
+
+## Data structure
+
+Currently based on the the [BIDS extension BEP001](https://github.com/bids-standard/bep001).
+
+Some required fields in the json files from the BEP extension were not added yet.
+
+The suffix `MP2RAGE` was added to the `.bidsignore` to pass the bids-validator test.
+
+Reminder
+```
+sub-01_inv-1_part-mag_MP2RAGE.nii.gz
+sub-01_inv-1_part-phase_MP2RAGE.nii.gz
+sub-01_inv-1_MP2RAGE.json
+sub-01_inv-2_part-mag_MP2RAGE.nii.gz
+sub-01_inv-2_part-phase_MP2RAGE.nii.gz
+sub-01_inv-2_MP2RAGE.json
+
+```

rawdata/.bidsignore

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+
+*_MP2RAGE.*

rawdata/CHANGES

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+0.0.1 2020-05
+
+  -  initial release

rawdata/README

@@ -0,0 +1,24 @@
+# README
+
+## Content
+
+This contains an high-res (0.7 mm) MP2RAGE of yours truly.
+
+## Data structure
+
+Currently based on the the [BIDS extension BEP001](https://github.com/bids-standard/bep001).
+
+Some required fields in the json files from the BEP extension were not added yet.
+
+The suffix `MP2RAGE` was added to the `.bidsignore` to pass the bids-validator test.
+
+Reminder
+```
+sub-01_inv-1_part-mag_MP2RAGE.nii.gz
+sub-01_inv-1_part-phase_MP2RAGE.nii.gz
+sub-01_inv-1_MP2RAGE.json
+sub-01_inv-2_part-mag_MP2RAGE.nii.gz
+sub-01_inv-2_part-phase_MP2RAGE.nii.gz
+sub-01_inv-2_MP2RAGE.json
+
+```

rawdata/T1map.json

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+{
+    "EstimationMethod": "Marques et al., 2013",
+    "BasedOn": [
+        "anat/sub-01_inv1_part-mag_MPRAGE.nii.gz",
+        "anat/sub-01_inv1_part-phase_MPRAGE.nii.gz",
+        "anat/sub-01_inv2_part-mag_MPRAGE.nii.gz",
+        "anat/sub-01_inv2_part-phase_MPRAGE.nii.gz"
+    ],
+    "MagneticFieldStrength": "7",
+    "ExcitationRepetitionTime": "",
+    "InversionRepetitionTime": "",
+    "NumberShots": "",
+    "PartialFourier": "",
+    "Manufacturer": "SIEMENS",
+    "ManufacturersModelName": "Investigational_Device_7T",
+    "DeviceSerialNumber": "18919",
+    "SoftwareVersions": "syngo MR B17",
+    "StationName": "",
+    "InstitutionName": "MPI Leipzig",
+    "InstitutionAddress": "Stephanstrasse 1a,Leipzig-FD201D-,Leipzig,DE,04103",
+    "InstitutionalDepartmentName": "",
+    "ReceiveCoilName": "",
+    "ReceiveCoilActiveElements": "",
+    "GradientSetType": "",
+    "MRTransmitCoilSequence": "",
+    "MatrixCoilMode": "",
+    "CoilCombinationMethod": "",
+    "NonlinearGradientCorrection": "",
+    "WaterFatShift": "",
+    "EchoTrainLength": "",
+    "DwellTime": "",
+    "MultibandAccelerationFactor": "",
+    "AnatomicalLandmarkCoordinates": "",
+    "MRAcquisitionType": "3D",
+    "ScanningSequence": "GR IR",
+    "SequenceVariant": "SP MP",
+    "ScanOptions": "IR PFP WE",
+    "SequenceName": "tfl3d1_ns",
+    "PulseSequenceType": "MP2RAGE",
+    "PulseSequenceDetails": "",
+    "ParallelReductionFactorInPlane": "",
+    "ParallelAcquisitionTechnique": "",
+    "PartialFourierDirection": "",
+    "EffectiveEchoSpacing": "",
+    "TotalReadoutTime": "",
+    "PhaseEncodingDirection": "y-",
+    "EchoTime1": "0.00245",
+    "EchoTime2": "0.01",
+    "SliceThickness": "0.69999999"
+}

rawdata/T1w.json

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+{
+    "EstimationMethod": "Marques et al., 2013",
+    "BasedOn": [
+        "anat/sub-01_inv1_part-mag_MPRAGE.nii.gz",
+        "anat/sub-01_inv1_part-phase_MPRAGE.nii.gz",
+        "anat/sub-01_inv2_part-mag_MPRAGE.nii.gz",
+        "anat/sub-01_inv2_part-phase_MPRAGE.nii.gz"
+    ],
+    "MagneticFieldStrength": "7",
+    "ExcitationRepetitionTime": "",
+    "InversionRepetitionTime": "",
+    "NumberShots": "",
+    "PartialFourier": "",
+    "Manufacturer": "SIEMENS",
+    "ManufacturersModelName": "Investigational_Device_7T",
+    "DeviceSerialNumber": "18919",
+    "SoftwareVersions": "syngo MR B17",
+    "StationName": "",
+    "InstitutionName": "MPI Leipzig",
+    "InstitutionAddress": "Stephanstrasse 1a,Leipzig-FD201D-,Leipzig,DE,04103",
+    "InstitutionalDepartmentName": "",
+    "ReceiveCoilName": "",
+    "ReceiveCoilActiveElements": "",
+    "GradientSetType": "",
+    "MRTransmitCoilSequence": "",
+    "MatrixCoilMode": "",
+    "CoilCombinationMethod": "",
+    "NonlinearGradientCorrection": "",
+    "WaterFatShift": "",
+    "EchoTrainLength": "",
+    "DwellTime": "",
+    "MultibandAccelerationFactor": "",
+    "AnatomicalLandmarkCoordinates": "",
+    "MRAcquisitionType": "3D",
+    "ScanningSequence": "GR IR",
+    "SequenceVariant": "SP MP",
+    "ScanOptions": "IR PFP WE",
+    "SequenceName": "tfl3d1_ns",
+    "PulseSequenceType": "MP2RAGE",
+    "PulseSequenceDetails": "",
+    "ParallelReductionFactorInPlane": "",
+    "ParallelAcquisitionTechnique": "",
+    "PartialFourierDirection": "",
+    "EffectiveEchoSpacing": "",
+    "TotalReadoutTime": "",
+    "PhaseEncodingDirection": "y-",
+    "EchoTime1": "0.00245",
+    "EchoTime2": "0.01",
+    "SliceThickness": "0.69999999"
+}

rawdata/dataset_description.json

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+{
+    "Name": "remi gau high res",
+    "BIDSVersion": "1.0.10",
+    "Authors": [
+        "Remi Gau",
+				"Uta Noppeney"
+    ],
+		"License": "CC0 1.0",
+		"Acknowledgements": "",
+		"HowToAcknowledge": "",
+		"Funding": [
+				"ERC",
+				"MPI"
+		],
+		"DatasetDOI": "",
+    "Description": "Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum."
+}

rawdata/sub-01/anat/sub-01_MP2RAGE.json

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+{
+  "MagneticFieldStrength": "7",
+  "ExcitationRepetitionTime": "",
+  "InversionRepetitionTime": "",
+  "NumberShots": "",
+  "PartialFourier": "",
+  "Manufacturer": "SIEMENS",
+  "ManufacturersModelName": "Investigational_Device_7T",
+  "DeviceSerialNumber": "18919",
+  "SoftwareVersions": "syngo MR B17",
+  "StationName": "",
+  "InstitutionName": "MPI Leipzig",
+  "InstitutionAddress": "Stephanstrasse 1a,Leipzig-FD201D-,Leipzig,DE,04103",
+  "InstitutionalDepartmentName": "",
+  "ReceiveCoilName": "",
+  "ReceiveCoilActiveElements": "",
+  "GradientSetType": "",
+  "MRTransmitCoilSequence": "",
+  "MatrixCoilMode": "",
+  "CoilCombinationMethod": "",
+  "NonlinearGradientCorrection": "",
+  "WaterFatShift": "",
+  "EchoTrainLength": "",
+  "DwellTime": "",
+  "MultibandAccelerationFactor": "",
+  "AnatomicalLandmarkCoordinates": "",
+  "MRAcquisitionType": "3D",
+  "ScanningSequence": "GR IR",
+  "SequenceVariant": "SP MP",
+  "ScanOptions": "IR PFP WE",
+  "SequenceName": "tfl3d1_ns",
+  "PulseSequenceType": "MP2RAGE",
+  "PulseSequenceDetails": "",
+  "ParallelReductionFactorInPlane": "",
+  "ParallelAcquisitionTechnique": "",
+  "PartialFourierDirection": "",
+  "EffectiveEchoSpacing": "",
+  "TotalReadoutTime": "",
+  "PhaseEncodingDirection": "y-",
+  "EchoTime1": "0.00245",
+  "EchoTime2": "0.01",
+  "SliceThickness": "0.69999999"
+}

rawdata/sub-01/anat/sub-01_T1map.nii

@@ -0,0 +1 @@
+../../../.git/annex/objects/Jp/Kw/MD5E-s49152352--f7f439220ea8fc56c89d20ab146fda54.nii/MD5E-s49152352--f7f439220ea8fc56c89d20ab146fda54.nii

rawdata/sub-01/anat/sub-01_T1w.nii

@@ -0,0 +1 @@
+../../../.git/annex/objects/Zq/X8/MD5E-s49152352--d53d98976b3d519cef1c52424ce0631b.nii/MD5E-s49152352--d53d98976b3d519cef1c52424ce0631b.nii

rawdata/sub-01/anat/sub-01_inv-1_MP2RAGE.json

@@ -0,0 +1,4 @@
+{
+    "InversionTime": "900",
+    "FlipAngle": "5"
+}

rawdata/sub-01/anat/sub-01_inv-1_part-mag_MP2RAGE.nii

@@ -0,0 +1 @@
+../../../.git/annex/objects/9j/FG/MD5E-s49152352--c06c2069de6414815b2a883d4a0fa360.nii/MD5E-s49152352--c06c2069de6414815b2a883d4a0fa360.nii

rawdata/sub-01/anat/sub-01_inv-1_part-phase_MP2RAGE.nii

@@ -0,0 +1 @@
+../../../.git/annex/objects/WM/Vz/MD5E-s49152352--0a7451d0a6c53ccb8cbe2298b724ab46.nii/MD5E-s49152352--0a7451d0a6c53ccb8cbe2298b724ab46.nii

rawdata/sub-01/anat/sub-01_inv-2_MP2RAGE.json

@@ -0,0 +1,4 @@
+{
+    "InversionTime": "2750",
+    "FlipAngle": "3"
+}

rawdata/sub-01/anat/sub-01_inv-2_part-mag_MP2RAGE.nii

@@ -0,0 +1 @@
+../../../.git/annex/objects/1x/3Q/MD5E-s49152352--32ed33cf43b071ddde0a17857fecf672.nii/MD5E-s49152352--32ed33cf43b071ddde0a17857fecf672.nii

rawdata/sub-01/anat/sub-01_inv-2_part-phase_MP2RAGE.nii

@@ -0,0 +1 @@
+../../../.git/annex/objects/50/Zx/MD5E-s49152352--257d362d70ed1df7cf4b473cadb952a5.nii/MD5E-s49152352--257d362d70ed1df7cf4b473cadb952a5.nii