diff --git a/BIDS_Dataset/README b/BIDS_Dataset/README deleted file mode 100644 index f96d811a8..000000000 --- a/BIDS_Dataset/README +++ /dev/null @@ -1,10 +0,0 @@ -Heavily downsampled CS-DSI testing datasets - -This data has had some parameters changed so that there are different -parameter groups in the same key groups. - -## Changes - - - sub-01_ses-phdiff_acq-HASC55AP_dwi: EchoTime set to 0.04 from 0.089 - - sub-02_ses-phdiff_task-rest_bold: Fieldmap has been removed - - sub-03_ses-phdiff_task-rest_bold: FlipAngle set to 70 from 90 diff --git a/BIDS_Dataset/dataset_description.json b/BIDS_Dataset/dataset_description.json deleted file mode 100644 index 9ee88dbcc..000000000 --- a/BIDS_Dataset/dataset_description.json +++ /dev/null @@ -1,7 +0,0 @@ -{ - "BIDSVersion": "1.0.0", - "License": "BSD 3-clause", - "Name": "Heavily downsampled CS-DSI simulated data", - "ReferencesAndLinks": [], - "Authors": ["PennLINC", "PennBBL"] -} diff --git a/BIDS_Dataset/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.json b/BIDS_Dataset/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.json deleted file mode 100644 index b8005d8af..000000000 --- a/BIDS_Dataset/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.json +++ /dev/null @@ -1,34 +0,0 @@ -{ - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "AcquisitionNumber": 1, - "InstitutionName": "HUP", - "InstitutionAddress": "Spruce_Street_3400_Philadelphia_Pennsylvania_US_19104", - "DeviceSerialNumber": "167024", - "SoftwareVersions": "syngo_MR_E11", - "ProcedureStepDescription": "MR_HEAD_WO_IV_CONTRAST", - "ScanningSequence": "GR_IR", - "SequenceVariant": "SK_SP_MP", - "SeriesDescription": "ABCD_T1w_MPR_vNav", - "BodyPartExamined": "BRAIN", - "ProtocolName": "ABCD_T1w_MPR_vNav", - "PatientName": "John Doe", - "SequenceName": "tfl3d1_16ns", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "M", - "ND", - "NORM" - ], - "AcquisitionTime": "16:15:31.770000", - "MagneticFieldStrength": 3, - "FlipAngle": 8, - "EchoTime": 0.0029, - "RepetitionTime": 2.5, - "InversionTime": 1.07, - "PhaseEncodingLines": 256, - "PhaseEncodingDirection": "i-", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20170724 (OpenJPEG build) GCC6.1.0" -} diff --git a/BIDS_Dataset/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.nii.gz b/BIDS_Dataset/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.nii.gz deleted file mode 100644 index 5dd2f5e70..000000000 Binary files a/BIDS_Dataset/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.nii.gz and /dev/null differ diff --git a/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bval b/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bval deleted file mode 100644 index b0e700029..000000000 --- a/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bval +++ /dev/null @@ -1 +0,0 @@ -0 0 2000 3780 3800 4380 2195 2205 4200 3570 diff --git a/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bvec b/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bvec deleted file mode 100644 index 14ebd3001..000000000 --- a/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bvec +++ /dev/null @@ -1,3 +0,0 @@ -0 0 0.947306 -0.689491 -0.687391 -0.640236 0.904801 0.301134 0.218033 0.236237 -0 0 -0.320301 -0.233031 0.690471 -0.429664 -0.305819 -0.906545 0.874886 0.239537 -0 0 -0.00426696 -0.685783 -0.225265 -0.636779 -0.296327 -0.295796 -0.432477 -0.941708 \ No newline at end of file diff --git a/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.json b/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.json deleted file mode 100644 index f6cf3ab19..000000000 --- a/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "ProcedureStepDescription": "MR_HEAD_WO_IV_CONTRAST", - "DeviceSerialNumber": "167024", - "EffectiveEchoSpacing": 0.000689998, - "TotalReadoutTime": 0.0717598, - "ManufacturersModelName": "Prisma_fit", - "ProtocolName": "ABCD_dMRI", - "BandwidthPerPixelPhaseEncode": 10.352, - "PhaseEncodingLines": 140, - "RepetitionTime": 4.2, - "EchoTrainLength": 105, - "MagneticFieldStrength": 3, - "AcquisitionNumber": 1, - "InstitutionName": "HUP", - "BodyPartExamined": "BRAIN", - "ConversionSoftware": "dcm2niix", - "ScanningSequence": "EP", - "Manufacturer": "Siemens", - "FlipAngle": 90, - "ConversionSoftwareVersion": "v1.0.20170724 (OpenJPEG build) GCC6.1.0", - "SeriesDescription": "ABCD_dMRI", - "InstitutionAddress": "Spruce_Street_3400_Philadelphia_Pennsylvania_US_19104", - "AcquisitionTime": "16:31:6.145000", - "SequenceName": "ep_b0", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "DIFFUSION", - "NONE", - "ND", - "MOSAIC" - ], - "EchoTime": 0.089, - "SequenceVariant": "SK_SP", - "SliceTiming": [ - 0.0, - 0.11666666666666667, - 0.23333333333333334, - 0.35, - 0.4666666666666667, - 0.5833333333333334, - 0.7, - 0.8166666666666667, - 0.9333333333333333, - 1.05, - 1.1666666666666667, - 1.2833333333333334, - 1.4, - 1.5166666666666666, - 1.6333333333333333, - 1.75, - 1.8666666666666667, - 1.9833333333333334, - 2.1, - 2.216666666666667, - 2.3333333333333335, - 2.45, - 2.566666666666667, - 2.6833333333333336, - 2.8, - 2.9166666666666665, - 3.033333333333333, - 3.15, - 3.2666666666666666, - 3.3833333333333333, - 3.5, - 3.6166666666666667, - 3.7333333333333334, - 3.85, - 3.966666666666667, - 4.083333333333333 - ], - "PhaseEncodingDirection": "j", - "SoftwareVersions": "syngo_MR_E11" -} diff --git a/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz b/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz deleted file mode 100644 index 78b43ef68..000000000 Binary files a/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz and /dev/null differ diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.json b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.json deleted file mode 100644 index 179945b6b..000000000 --- a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.json +++ /dev/null @@ -1,67 +0,0 @@ -{ - "AcquisitionMatrixPE": 64, - "AcquisitionNumber": 1, - "BaseResolution": 64, - "BodyPartExamined": "BRAIN", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180622 GCC6.3.0", - "EchoTime": 0.004, - "FlipAngle": 60, - "ImageOrientationPatientDICOM": [ - 1, - 0, - 0, - 0, - 1, - 0 - ], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "M", - "ND" - ], - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionName": "HUP6", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "Modality": "MR", - "PartialFourier": 0.75, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 48, - "PhaseResolution": 1, - "PixelBandwidth": 500, - "ProtocolName": "B0map_v4", - "PulseSequenceDetails": "%SiemensSeq%_gre_field_mapping", - "ReceiveCoilActiveElements": "HEA;HEP", - "ReceiveCoilName": "Head_32", - "ReconMatrixPE": 64, - "RepetitionTime": 1.5, - "SAR": 0.0935879, - "ScanOptions": "PFP_FS", - "ScanningSequence": "GR", - "SequenceName": "_fm2d2", - "SequenceVariant": "SP", - "SeriesDescription": "B0map_v4", - "SeriesNumber": 7, - "ShimSetting": [ - 1747, - -3883, - -285, - 583, - 125, - -23, - -45, - -40 - ], - "SliceThickness": 4, - "SoftwareVersions": "syngo_MR_E11", - "SpacingBetweenSlices": 4, - "StationName": "HUP_FNDBA_MR2", - "TxRefAmp": 220.327 -} diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.nii.gz b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.nii.gz deleted file mode 100644 index 8a7f44f4d..000000000 Binary files a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.nii.gz and /dev/null differ diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.json b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.json deleted file mode 100644 index 370334c18..000000000 --- a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.json +++ /dev/null @@ -1,68 +0,0 @@ -{ - "AcquisitionMatrixPE": 64, - "AcquisitionNumber": 1, - "BaseResolution": 64, - "BodyPartExamined": "BRAIN", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180622 GCC6.3.0", - "EchoNumber": 2, - "EchoTime": 0.00646, - "FlipAngle": 60, - "ImageOrientationPatientDICOM": [ - 1, - 0, - 0, - 0, - 1, - 0 - ], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "M", - "ND" - ], - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionName": "HUP6", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "Modality": "MR", - "PartialFourier": 0.75, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 48, - "PhaseResolution": 1, - "PixelBandwidth": 500, - "ProtocolName": "B0map_v4", - "PulseSequenceDetails": "%SiemensSeq%_gre_field_mapping", - "ReceiveCoilActiveElements": "HEA;HEP", - "ReceiveCoilName": "Head_32", - "ReconMatrixPE": 64, - "RepetitionTime": 1.5, - "SAR": 0.0935879, - "ScanOptions": "PFP_FS", - "ScanningSequence": "GR", - "SequenceName": "_fm2d2", - "SequenceVariant": "SP", - "SeriesDescription": "B0map_v4", - "SeriesNumber": 7, - "ShimSetting": [ - 1747, - -3883, - -285, - 583, - 125, - -23, - -45, - -40 - ], - "SliceThickness": 4, - "SoftwareVersions": "syngo_MR_E11", - "SpacingBetweenSlices": 4, - "StationName": "HUP_FNDBA_MR2", - "TxRefAmp": 220.327 -} diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.nii.gz b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.nii.gz deleted file mode 100644 index 4a99378f3..000000000 Binary files a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.nii.gz and /dev/null differ diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.json b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.json deleted file mode 100644 index 849f6a3b3..000000000 --- a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.json +++ /dev/null @@ -1,71 +0,0 @@ -{ - "IntendedFor": [ - "ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz" - ], - "AcquisitionMatrixPE": 64, - "AcquisitionNumber": 1, - "BaseResolution": 64, - "BodyPartExamined": "BRAIN", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180622 GCC6.3.0", - "EchoNumber": 2, - "EchoTime1": 0.004, - "EchoTime2": 0.00646, - "FlipAngle": 60, - "ImageOrientationPatientDICOM": [ - 1, - 0, - 0, - 0, - 1, - 0 - ], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND" - ], - "InPlanePhaseEncodingDirectionDICOM": "COL", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "Modality": "MR", - "PartialFourier": 0.75, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 48, - "PhaseResolution": 1, - "PixelBandwidth": 500, - "ProtocolName": "B0map_v4", - "PulseSequenceDetails": "%SiemensSeq%_gre_field_mapping", - "ReceiveCoilActiveElements": "HEA;HEP", - "ReceiveCoilName": "Head_32", - "ReconMatrixPE": 64, - "RepetitionTime": 1.5, - "SAR": 0.0935879, - "ScanOptions": "PFP_FS", - "ScanningSequence": "GR", - "SequenceName": "_fm2d2", - "SequenceVariant": "SP", - "SeriesDescription": "B0map_v4", - "SeriesNumber": 8, - "ShimSetting": [ - 1747, - -3883, - -285, - 583, - 125, - -23, - -45, - -40 - ], - "SliceThickness": 4, - "SoftwareVersions": "syngo_MR_E11", - "SpacingBetweenSlices": 4, - "StationName": "HUP_FNDBA_MR2", - "TxRefAmp": 220.327 -} diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.nii.gz b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.nii.gz deleted file mode 100644 index daf5e956e..000000000 Binary files a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.nii.gz and /dev/null differ diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_dir-PA_epi.json b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_dir-PA_epi.json deleted file mode 100644 index 6fd8eefc8..000000000 --- a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_dir-PA_epi.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "ProcedureStepDescription": "MR_HEAD_WO_IV_CONTRAST", - "DeviceSerialNumber": "167024", - "EffectiveEchoSpacing": 0.000689998, - "TotalReadoutTime": 0.0717598, - "ManufacturersModelName": "Prisma_fit", - "ProtocolName": "ABCD_dMRI", - "BandwidthPerPixelPhaseEncode": 10.352, - "PhaseEncodingLines": 140, - "RepetitionTime": 4.2, - "EchoTrainLength": 105, - "MagneticFieldStrength": 3, - "AcquisitionNumber": 1, - "InstitutionName": "HUP", - "BodyPartExamined": "BRAIN", - "ConversionSoftware": "dcm2niix", - "ScanningSequence": "EP", - "Manufacturer": "Siemens", - "FlipAngle": 90, - "InstitutionAddress": "Spruce_Street_3400_Philadelphia_Pennsylvania_US_19104", - "SeriesDescription": "ABCD_dMRI", - "ConversionSoftwareVersion": "v1.0.20170724 (OpenJPEG build) GCC6.1.0", - "AcquisitionTime": "16:31:6.145000", - "SequenceName": "ep_b0", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "DIFFUSION", - "NONE", - "ND", - "MOSAIC" - ], - "EchoTime": 0.089, - "SequenceVariant": "SK_SP", - "SliceTiming": [ - 0.0, - 0.11666666666666667, - 0.23333333333333334, - 0.35, - 0.4666666666666667, - 0.5833333333333334, - 0.7, - 0.8166666666666667, - 0.9333333333333333, - 1.05, - 1.1666666666666667, - 1.2833333333333334, - 1.4, - 1.5166666666666666, - 1.6333333333333333, - 1.75, - 1.8666666666666667, - 1.9833333333333334, - 2.1, - 2.216666666666667, - 2.3333333333333335, - 2.45, - 2.566666666666667, - 2.6833333333333336, - 2.8, - 2.9166666666666665, - 3.033333333333333, - 3.15, - 3.2666666666666666, - 3.3833333333333333, - 3.5, - 3.6166666666666667, - 3.7333333333333334, - 3.85, - 3.966666666666667, - 4.083333333333333 - ], - "PhaseEncodingDirection": "j-", - "SoftwareVersions": "syngo_MR_E11", - "IntendedFor": [ - "ses-phdiff/func/sub-01_ses-phdiff_task-rest_bold.nii.gz" - ] -} diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_dir-PA_epi.nii.gz b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_dir-PA_epi.nii.gz deleted file mode 100644 index b60186d5a..000000000 Binary files a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_dir-PA_epi.nii.gz and /dev/null differ diff --git a/BIDS_Dataset/sub-01/ses-phdiff/func/sub-01_ses-phdiff_task-rest_bold.json b/BIDS_Dataset/sub-01/ses-phdiff/func/sub-01_ses-phdiff_task-rest_bold.json deleted file mode 100644 index 008c2809b..000000000 --- a/BIDS_Dataset/sub-01/ses-phdiff/func/sub-01_ses-phdiff_task-rest_bold.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "ProcedureStepDescription": "MR_HEAD_WO_IV_CONTRAST", - "DeviceSerialNumber": "167024", - "EffectiveEchoSpacing": 0.000689998, - "TotalReadoutTime": 0.0717598, - "ManufacturersModelName": "Prisma_fit", - "ProtocolName": "ABCD_dMRI", - "PatientName": "John Doe", - "TaskName": "rest", - "BandwidthPerPixelPhaseEncode": 10.352, - "PhaseEncodingLines": 140, - "RepetitionTime": 1.0, - "EchoTrainLength": 105, - "MagneticFieldStrength": 3, - "AcquisitionNumber": 1, - "InstitutionName": "HUP", - "BodyPartExamined": "BRAIN", - "ConversionSoftware": "dcm2niix", - "ScanningSequence": "EP", - "Manufacturer": "Siemens", - "FlipAngle": 90, - "ConversionSoftwareVersion": "v1.0.20170724 (OpenJPEG build) GCC6.1.0", - "SeriesDescription": "ABCD_dMRI", - "InstitutionAddress": "Spruce_Street_3400_Philadelphia_Pennsylvania_US_19104", - "AcquisitionTime": "16:31:6.145000", - "SequenceName": "ep_b0", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "DIFFUSION", - "NONE", - "ND", - "MOSAIC" - ], - "EchoTime": 0.089, - "SequenceVariant": "SK_SP", - "SliceTiming": [ - 0.0, - 0.027131782945736437, - 0.054263565891472874, - 0.0813953488372093, - 0.10852713178294575, - 0.1356589147286822, - 0.1627906976744186, - 0.18992248062015504, - 0.2170542635658915, - 0.24418604651162792, - 0.2713178294573644, - 0.2984496124031008, - 0.3255813953488372, - 0.35271317829457366, - 0.3798449612403101, - 0.4069767441860465, - 0.434108527131783, - 0.4612403100775194, - 0.48837209302325585, - 0.5155038759689923, - 0.5426356589147288, - 0.5697674418604651, - 0.5968992248062016, - 0.6240310077519381, - 0.6511627906976744, - 0.6782945736434108, - 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"AcquisitionNumber": 1, - "InstitutionName": "HUP", - "InstitutionAddress": "Spruce_Street_3400_Philadelphia_Pennsylvania_US_19104", - "DeviceSerialNumber": "167024", - "SoftwareVersions": "syngo_MR_E11", - "ProcedureStepDescription": "MR_HEAD_WO_IV_CONTRAST", - "ScanningSequence": "GR_IR", - "SequenceVariant": "SK_SP_MP", - "SeriesDescription": "ABCD_T1w_MPR_vNav", - "BodyPartExamined": "BRAIN", - "ProtocolName": "ABCD_T1w_MPR_vNav", - "SequenceName": "tfl3d1_16ns", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "M", - "ND", - "NORM" - ], - "AcquisitionTime": "16:15:31.770000", - "MagneticFieldStrength": 3, - "FlipAngle": 8, - "EchoTime": 0.0029, - "RepetitionTime": 2.5, - "InversionTime": 1.07, - "PhaseEncodingLines": 256, - "PhaseEncodingDirection": "i-", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20170724 (OpenJPEG build) GCC6.1.0" -} diff --git a/BIDS_Dataset/sub-02/ses-phdiff/anat/sub-02_ses-phdiff_T1w.nii.gz 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a/BIDS_Dataset/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_magnitude2.json +++ /dev/null @@ -1,68 +0,0 @@ -{ - "AcquisitionMatrixPE": 64, - "AcquisitionNumber": 1, - "BaseResolution": 64, - "BodyPartExamined": "BRAIN", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180622 GCC6.3.0", - "EchoNumber": 2, - "EchoTime": 0.00646, - "FlipAngle": 60, - "ImageOrientationPatientDICOM": [ - 1, - 0, - 0, - 0, - 1, - 0 - ], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "M", - "ND" - ], - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionName": "HUP6", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "Modality": "MR", - "PartialFourier": 0.75, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 48, - "PhaseResolution": 1, - "PixelBandwidth": 500, - "ProtocolName": 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a/BIDS_Dataset/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_phasediff.json b/BIDS_Dataset/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_phasediff.json deleted file mode 100644 index e13c68063..000000000 --- a/BIDS_Dataset/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_phasediff.json +++ /dev/null @@ -1,71 +0,0 @@ -{ - "IntendedFor": [ - "ses-phdiff/dwi/sub-03_ses-phdiff_acq-HASC55AP_dwi.nii.gz" - ], - "AcquisitionMatrixPE": 64, - "AcquisitionNumber": 1, - "BaseResolution": 64, - "BodyPartExamined": "BRAIN", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180622 GCC6.3.0", - "EchoNumber": 2, - "EchoTime1": 0.004, - "EchoTime2": 0.00646, - "FlipAngle": 60, - "ImageOrientationPatientDICOM": [ - 1, - 0, - 0, - 0, - 1, - 0 - ], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND" - ], - "InPlanePhaseEncodingDirectionDICOM": "COL", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "Modality": "MR", - "PartialFourier": 0.75, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 48, - "PhaseResolution": 1, - "PixelBandwidth": 500, - "ProtocolName": "B0map_v4", - "PulseSequenceDetails": "%SiemensSeq%_gre_field_mapping", - "ReceiveCoilActiveElements": "HEA;HEP", - "ReceiveCoilName": "Head_32", - "ReconMatrixPE": 64, - "RepetitionTime": 1.5, - "SAR": 0.0935879, - "ScanOptions": "PFP_FS", - "ScanningSequence": "GR", - "SequenceName": "_fm2d2", - "SequenceVariant": "SP", - "SeriesDescription": "B0map_v4", - "SeriesNumber": 8, - "ShimSetting": [ - 1747, - -3883, - -285, - 583, - 125, - -23, - -45, - -40 - ], - "SliceThickness": 4, - "SoftwareVersions": "syngo_MR_E11", - "SpacingBetweenSlices": 4, - "StationName": "HUP_FNDBA_MR2", - "TxRefAmp": 220.327 -} diff --git a/BIDS_Dataset/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_phasediff.nii.gz b/BIDS_Dataset/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_phasediff.nii.gz deleted file mode 100644 index daf5e956e..000000000 Binary files a/BIDS_Dataset/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_phasediff.nii.gz and /dev/null differ diff --git a/BIDS_Dataset/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_dir-PA_epi.json b/BIDS_Dataset/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_dir-PA_epi.json deleted file mode 100644 index c000ebb6c..000000000 --- a/BIDS_Dataset/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_dir-PA_epi.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "ProcedureStepDescription": "MR_HEAD_WO_IV_CONTRAST", - "DeviceSerialNumber": "167024", - "EffectiveEchoSpacing": 0.000689998, - "TotalReadoutTime": 0.0717598, - "ManufacturersModelName": "Prisma_fit", - "ProtocolName": "ABCD_dMRI", - "BandwidthPerPixelPhaseEncode": 10.352, - "PhaseEncodingLines": 140, - "RepetitionTime": 4.2, - "EchoTrainLength": 105, - "MagneticFieldStrength": 3, - "AcquisitionNumber": 1, - "InstitutionName": 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-{ - "ProcedureStepDescription": "MR_HEAD_WO_IV_CONTRAST", - "DeviceSerialNumber": "167024", - "EffectiveEchoSpacing": 0.000689998, - "TotalReadoutTime": 0.0717598, - "ManufacturersModelName": "Prisma_fit", - "ProtocolName": "ABCD_dMRI", - "TaskName": "rest", - "BandwidthPerPixelPhaseEncode": 10.352, - "PhaseEncodingLines": 140, - "RepetitionTime": 1.0, - "EchoTrainLength": 105, - "MagneticFieldStrength": 3, - "AcquisitionNumber": 1, - "InstitutionName": "HUP", - "BodyPartExamined": "BRAIN", - "ConversionSoftware": "dcm2niix", - "ScanningSequence": "EP", - "Manufacturer": "Siemens", - "FlipAngle": 70, - "ConversionSoftwareVersion": "v1.0.20170724 (OpenJPEG build) GCC6.1.0", - "SeriesDescription": "ABCD_dMRI", - "InstitutionAddress": "Spruce_Street_3400_Philadelphia_Pennsylvania_US_19104", - "AcquisitionTime": "16:31:6.145000", - "SequenceName": "ep_b0", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "DIFFUSION", - "NONE", - "ND", - "MOSAIC" - ], - "EchoTime": 0.089, - "SequenceVariant": 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a/BIDS_Dataset/sub-04/ses-phdiff/fmap/sub-04_ses-phdiff_acq-v4_magnitude1.json b/BIDS_Dataset/sub-04/ses-phdiff/fmap/sub-04_ses-phdiff_acq-v4_magnitude1.json deleted file mode 100644 index 179945b6b..000000000 --- a/BIDS_Dataset/sub-04/ses-phdiff/fmap/sub-04_ses-phdiff_acq-v4_magnitude1.json +++ /dev/null @@ -1,67 +0,0 @@ -{ - "AcquisitionMatrixPE": 64, - "AcquisitionNumber": 1, - "BaseResolution": 64, - "BodyPartExamined": "BRAIN", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180622 GCC6.3.0", - "EchoTime": 0.004, - "FlipAngle": 60, - "ImageOrientationPatientDICOM": [ - 1, - 0, - 0, - 0, - 1, - 0 - ], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "M", - "ND" - ], - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionName": "HUP6", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "Modality": "MR", - "PartialFourier": 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index 8a7f44f4d..000000000 Binary files a/BIDS_Dataset/sub-04/ses-phdiff/fmap/sub-04_ses-phdiff_acq-v4_magnitude1.nii.gz and /dev/null differ diff --git a/BIDS_Dataset/sub-04/ses-phdiff/fmap/sub-04_ses-phdiff_acq-v4_magnitude2.json b/BIDS_Dataset/sub-04/ses-phdiff/fmap/sub-04_ses-phdiff_acq-v4_magnitude2.json deleted file mode 100644 index 370334c18..000000000 --- a/BIDS_Dataset/sub-04/ses-phdiff/fmap/sub-04_ses-phdiff_acq-v4_magnitude2.json +++ /dev/null @@ -1,68 +0,0 @@ -{ - "AcquisitionMatrixPE": 64, - "AcquisitionNumber": 1, - "BaseResolution": 64, - "BodyPartExamined": "BRAIN", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180622 GCC6.3.0", - "EchoNumber": 2, - "EchoTime": 0.00646, - "FlipAngle": 60, - "ImageOrientationPatientDICOM": [ - 1, - 0, - 0, - 0, - 1, - 0 - ], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "M", - "ND" - ], - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionName": 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a/BIDS_Dataset/sub-04/ses-phdiff/fmap/sub-04_ses-phdiff_acq-v4_magnitude2.nii.gz b/BIDS_Dataset/sub-04/ses-phdiff/fmap/sub-04_ses-phdiff_acq-v4_magnitude2.nii.gz deleted file mode 100644 index 4a99378f3..000000000 Binary files a/BIDS_Dataset/sub-04/ses-phdiff/fmap/sub-04_ses-phdiff_acq-v4_magnitude2.nii.gz and /dev/null differ diff --git a/BIDS_Dataset/sub-04/ses-phdiff/fmap/sub-04_ses-phdiff_acq-v4_phasediff.json b/BIDS_Dataset/sub-04/ses-phdiff/fmap/sub-04_ses-phdiff_acq-v4_phasediff.json deleted file mode 100644 index 234ac439d..000000000 --- a/BIDS_Dataset/sub-04/ses-phdiff/fmap/sub-04_ses-phdiff_acq-v4_phasediff.json +++ /dev/null @@ -1,71 +0,0 @@ -{ - "IntendedFor": [ - "ses-phdiff/dwi/sub-04_ses-phdiff_acq-HASC55AP_dwi.nii.gz" - ], - "AcquisitionMatrixPE": 64, - "AcquisitionNumber": 1, - "BaseResolution": 64, - "BodyPartExamined": "BRAIN", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180622 GCC6.3.0", 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/dev/null differ diff --git a/BIDS_Dataset/sub-04/ses-phdiff/func/sub-04_ses-phdiff_task-rest_bold.json b/BIDS_Dataset/sub-04/ses-phdiff/func/sub-04_ses-phdiff_task-rest_bold.json deleted file mode 100644 index 14dbbc97e..000000000 --- a/BIDS_Dataset/sub-04/ses-phdiff/func/sub-04_ses-phdiff_task-rest_bold.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "ProcedureStepDescription": "MR_HEAD_WO_IV_CONTRAST", - "DeviceSerialNumber": "167024", - "EffectiveEchoSpacing": 0.000689998, - "TotalReadoutTime": 0.0717598, - "ManufacturersModelName": "Prisma_fit", - "ProtocolName": "ABCD_dMRI", - "TaskName": "rest", - "BandwidthPerPixelPhaseEncode": 10.352, - "PhaseEncodingLines": 140, - "RepetitionTime": 1.0, - "EchoTrainLength": 105, - "MagneticFieldStrength": 3, - "AcquisitionNumber": 1, - "InstitutionName": "HUP", - "BodyPartExamined": "BRAIN", - "ConversionSoftware": "dcm2niix", - "ScanningSequence": "EP", - "Manufacturer": "Siemens", - "FlipAngle": 70, - "ConversionSoftwareVersion": "v1.0.20170724 (OpenJPEG build) GCC6.1.0", - "SeriesDescription": "ABCD_dMRI", - "InstitutionAddress": "Spruce_Street_3400_Philadelphia_Pennsylvania_US_19104", - "AcquisitionTime": "16:31:6.145000", - "SequenceName": "ep_b0", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "DIFFUSION", - "NONE", - "ND", - "MOSAIC" - ], - "EchoTime": 0.089, - "SequenceVariant": "SK_SP", - "SliceTiming": [ - 0.0, - 0.027131782945736437, - 0.054263565891472874, - 0.0813953488372093, - 0.10852713178294575, - 0.1356589147286822, - 0.1627906976744186, - 0.18992248062015504, - 0.2170542635658915, - 0.24418604651162792, - 0.2713178294573644, - 0.2984496124031008, - 0.3255813953488372, - 0.35271317829457366, - 0.3798449612403101, - 0.4069767441860465, - 0.434108527131783, - 0.4612403100775194, - 0.48837209302325585, - 0.5155038759689923, - 0.5426356589147288, - 0.5697674418604651, - 0.5968992248062016, - 0.6240310077519381, - 0.6511627906976744, - 0.6782945736434108, - 0.7054263565891473, - 0.7325581395348837, - 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CuBIDS_Toy_Dataset_Curation/v1_AcqGrouping.csv rename to cubids/tests/data/CuBIDS_Toy_Dataset_Curation/v1_AcqGrouping.csv diff --git a/CuBIDS_Toy_Dataset_Curation/v1_files.csv b/cubids/tests/data/CuBIDS_Toy_Dataset_Curation/v1_files.csv similarity index 100% rename from CuBIDS_Toy_Dataset_Curation/v1_files.csv rename to cubids/tests/data/CuBIDS_Toy_Dataset_Curation/v1_files.csv diff --git a/CuBIDS_Toy_Dataset_Curation/v1_summary.csv b/cubids/tests/data/CuBIDS_Toy_Dataset_Curation/v1_summary.csv similarity index 100% rename from CuBIDS_Toy_Dataset_Curation/v1_summary.csv rename to cubids/tests/data/CuBIDS_Toy_Dataset_Curation/v1_summary.csv diff --git a/CuBIDS_Toy_Dataset_Curation/v2_AcqGroupInfo.txt b/cubids/tests/data/CuBIDS_Toy_Dataset_Curation/v2_AcqGroupInfo.txt similarity index 100% rename from CuBIDS_Toy_Dataset_Curation/v2_AcqGroupInfo.txt rename to cubids/tests/data/CuBIDS_Toy_Dataset_Curation/v2_AcqGroupInfo.txt diff --git a/CuBIDS_Toy_Dataset_Curation/v2_AcqGrouping.csv 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cubids/tests/data/CuBIDS_Toy_Dataset_Curation/v2_summary.csv