diff --git a/.gitignore b/.gitignore index 82f9275..695e8fd 100644 --- a/.gitignore +++ b/.gitignore @@ -25,6 +25,8 @@ share/python-wheels/ .installed.cfg *.egg MANIFEST +.idea +.DS_Store # PyInstaller # Usually these files are written by a python script from a template diff --git a/tests/data/bids/.bids-validator-config.json b/tests/data/bids/.bids-validator-config.json new file mode 100644 index 0000000..0e23c2b --- /dev/null +++ b/tests/data/bids/.bids-validator-config.json @@ -0,0 +1,19 @@ +{ + "ignore": [ + "NIFTI_UNIT", + "INCONSISTENT_PARAMETERS", + "SLICE_TIMING_NOT_DEFINED", + "NIFTI_PIXDIM4", + "BOLD_NOT_4D", + "REPETITION_TIME_MUST_DEFINE", + "TASK_NAME_MUST_DEFINE", + "MISSING_SESSION", + "INCONSISTENT_SUBJECTS", + "SCANS_FILENAME_NOT_MATCH_DATASET", + "CUSTOM_COLUMN_WITHOUT_DESCRIPTION", + "NO_AUTHORS" + ], + "warn": [], + "error": [], + "ignoredFiles": [] +} \ No newline at end of file diff --git a/tests/data/bids/.bidsignore b/tests/data/bids/.bidsignore new file mode 100644 index 0000000..f02668a --- /dev/null +++ b/tests/data/bids/.bidsignore @@ -0,0 +1,2 @@ +swi/ +conversion_info/ \ No newline at end of file diff --git a/tests/data/bids/README b/tests/data/bids/README new file mode 100644 index 0000000..30085e4 --- /dev/null +++ b/tests/data/bids/README @@ -0,0 +1,2 @@ +This BIDS directory was generated with Clinica v0.7.4. +More information on https://www.clinica.run diff --git a/tests/data/bids/dataset_description.json b/tests/data/bids/dataset_description.json new file mode 100644 index 0000000..847d362 --- /dev/null +++ b/tests/data/bids/dataset_description.json @@ -0,0 +1,5 @@ +{ + "Name": "TEST", + "BIDSVersion": "1.10.0", + "DatasetType": "raw" +} diff --git a/tests/data/bids/participants.tsv b/tests/data/bids/participants.tsv new file mode 100644 index 0000000..3bc8dde --- /dev/null +++ b/tests/data/bids/participants.tsv @@ -0,0 +1,5 @@ +participant_id +sub-001 +sub-002 +sub-003 +sub-004 diff --git a/tests/data/bids/sub-001/ses-M000/anat/sub-001_ses-M000_T1w.json b/tests/data/bids/sub-001/ses-M000/anat/sub-001_ses-M000_T1w.json new file mode 100644 index 0000000..e058a05 --- /dev/null +++ b/tests/data/bids/sub-001/ses-M000/anat/sub-001_ses-M000_T1w.json @@ -0,0 +1,6 @@ +{ + "MRAcquisitionType": "3D", + "PulseSequenceType": "RM", + "Manufacturer": "GE MEDICAL SYSTEMS", + "MagneticFieldStrength": "1.5" +} \ No newline at end of file diff --git a/tests/data/bids/sub-001/ses-M000/anat/sub-001_ses-M000_T1w.nii.gz b/tests/data/bids/sub-001/ses-M000/anat/sub-001_ses-M000_T1w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-001/ses-M000/pet/sub-001_ses-M000_trc-18FFDG_rec-coregavg_pet.nii.gz b/tests/data/bids/sub-001/ses-M000/pet/sub-001_ses-M000_trc-18FFDG_rec-coregavg_pet.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-001/ses-M000/pet/sub-001_ses-M000_trc-18FFDG_rec-coregiso_pet.nii.gz b/tests/data/bids/sub-001/ses-M000/pet/sub-001_ses-M000_trc-18FFDG_rec-coregiso_pet.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-001/ses-M000/sub-001_ses-M000_scans.tsv b/tests/data/bids/sub-001/ses-M000/sub-001_ses-M000_scans.tsv new file mode 100644 index 0000000..10ef075 --- /dev/null +++ b/tests/data/bids/sub-001/ses-M000/sub-001_ses-M000_scans.tsv @@ -0,0 +1,4 @@ + filename scan_id mri_field acq_time +0 anat/sub-001_ses-M000_T1w.nii.gz 34316 1.5 2005-12-09 +1 pet/sub-001_ses-M000_trc-18FFDG_rec-coregavg_pet.nii.gz 26939 +2 pet/sub-001_ses-M000_trc-18FFDG_rec-coregiso_pet.nii.gz 26939 diff --git a/tests/data/bids/sub-001/ses-M156/anat/sub-001_ses-M156_FLAIR.json b/tests/data/bids/sub-001/ses-M156/anat/sub-001_ses-M156_FLAIR.json new file mode 100644 index 0000000..b56eead --- /dev/null +++ b/tests/data/bids/sub-001/ses-M156/anat/sub-001_ses-M156_FLAIR.json @@ -0,0 +1,52 @@ +{ + "Modality": "MR", + "ImagingFrequency": 127.704, + "PulseSequenceName": "CubeT2flair", + "ManufacturersModelName": "DISCOVERY MR750", + "InstitutionName": "UIRR", + "DeviceSerialNumber": "6cnQ6wuFVm2vRB7ybMfpFTk", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "27\\LX\\MR Software release:DV25.1_R03_1802.a", + "SeriesDescription": "Sagittal 3D FLAIR", + "ProtocolName": "ADNI3 Basic Human Protoc", + "ScanningSequence": "SE\\IR", + "SequenceVariant": "SK", + "ScanOptions": "SAT_GEMS\\EDR_GEMS\\FILTERED_GEMS\\ACC_GEMS\\FS", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "OTHER" + ], + "SeriesNumber": 5, + "AcquisitionTime": "10:16:36.000000", + "AcquisitionNumber": 1, + "SliceThickness": 1.2, + "SpacingBetweenSlices": 1.2, + "SAR": 0.718189, + "EchoTime": 0.11668, + "RepetitionTime": 4.8, + "InversionTime": 1.476, + "FlipAngle": 90, + "CoilString": "8HRBRAIN", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 182, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "ParallelReductionOutOfPlane": 2, + "PixelBandwidth": 244.141, + "PhaseEncodingAxis": "i", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505" +} \ No newline at end of file diff --git a/tests/data/bids/sub-001/ses-M156/anat/sub-001_ses-M156_FLAIR.nii.gz b/tests/data/bids/sub-001/ses-M156/anat/sub-001_ses-M156_FLAIR.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-001/ses-M156/anat/sub-001_ses-M156_T1w.json b/tests/data/bids/sub-001/ses-M156/anat/sub-001_ses-M156_T1w.json new file mode 100644 index 0000000..a9b9fb0 --- /dev/null +++ b/tests/data/bids/sub-001/ses-M156/anat/sub-001_ses-M156_T1w.json @@ -0,0 +1,6 @@ +{ + "MRAcquisitionType": "3D", + "PulseSequenceType": "GR", + "Manufacturer": "GE MEDICAL SYSTEMS", + "MagneticFieldStrength": "3.0" +} \ No newline at end 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0.87 0.328 -0.269 diff --git a/tests/data/bids/sub-001/ses-M156/dwi/sub-001_ses-M156_dwi.json b/tests/data/bids/sub-001/ses-M156/dwi/sub-001_ses-M156_dwi.json new file mode 100644 index 0000000..222a249 --- /dev/null +++ b/tests/data/bids/sub-001/ses-M156/dwi/sub-001_ses-M156_dwi.json @@ -0,0 +1,53 @@ +{ + "Modality": "MR", + "ImagingFrequency": 127.704, + "PulseSequenceName": "epi2", + "InternalPulseSequenceName": "EPI2", + "ManufacturersModelName": "DISCOVERY MR750", + "InstitutionName": "UIRR", + "DeviceSerialNumber": "6cnQ6wuFVm2vRB7ybMfpFTk", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "27\\LX\\MR Software release:DV25.1_R03_1802.a", + "SeriesDescription": "Axial DTI", + "ProtocolName": "ADNI3 Basic Human Protoc", + "ScanningSequence": "EP\\SE", + "SequenceVariant": "NONE", + "ScanOptions": "SAT_GEMS\\EPI_GEMS\\FILTERED_GEMS\\ACC_GEMS\\PFF\\FS", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "OTHER" + ], + "SeriesNumber": 8, + "AcquisitionTime": 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a/tests/data/bids/sub-001/ses-M156/func/sub-001_ses-M156_task-rest_bold.json b/tests/data/bids/sub-001/ses-M156/func/sub-001_ses-M156_task-rest_bold.json new file mode 100644 index 0000000..f7686ee --- /dev/null +++ b/tests/data/bids/sub-001/ses-M156/func/sub-001_ses-M156_task-rest_bold.json @@ -0,0 +1,103 @@ +{ + "Modality": "MR", + "ImagingFrequency": 127.704, + "PulseSequenceName": "epi", + "InternalPulseSequenceName": "EPI", + "ManufacturersModelName": "DISCOVERY MR750", + "InstitutionName": "UIRR", + "DeviceSerialNumber": "6cnQ6wuFVm2vRB7ybMfpFTk", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "27\\LX\\MR Software release:DV25.1_R03_1802.a", + "SeriesDescription": "Axial rsfMRI (Eyes Open)", + "ProtocolName": "ADNI3 Basic Human Protoc", + "ScanningSequence": "EP\\GR", + "SequenceVariant": "SS", + "ScanOptions": "MP_GEMS\\EPI_GEMS", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "OTHER" + ], + "SeriesNumber": 9, + "AcquisitionTime": 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"ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505" +} \ No newline at end of file diff --git a/tests/data/bids/sub-001/ses-M156/func/sub-001_ses-M156_task-rest_bold.nii.gz b/tests/data/bids/sub-001/ses-M156/func/sub-001_ses-M156_task-rest_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-001/ses-M156/pet/sub-001_ses-M156_trc-18FAV45_pet.nii.gz b/tests/data/bids/sub-001/ses-M156/pet/sub-001_ses-M156_trc-18FAV45_pet.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-001/ses-M156/sub-001_ses-M156_scans.tsv b/tests/data/bids/sub-001/ses-M156/sub-001_ses-M156_scans.tsv new file mode 100644 index 0000000..853c6d1 --- /dev/null +++ b/tests/data/bids/sub-001/ses-M156/sub-001_ses-M156_scans.tsv @@ -0,0 +1,11 @@ + filename scan_id mri_field acq_time +0 dwi/sub-001_ses-M156_dwi.json 1120329 +1 dwi/sub-001_ses-M156_dwi.nii.gz 1120329 +2 dwi/sub-001_ses-M156_dwi.bval 1120329 +3 dwi/sub-001_ses-M156_dwi.bvec 1120329 +4 anat/sub-001_ses-M156_FLAIR.nii.gz 1120322 3.0 +5 anat/sub-001_ses-M156_FLAIR.json 1120322 3.0 +6 anat/sub-001_ses-M156_T1w.nii.gz 1120324 3.0 2019-01-24 +7 pet/sub-001_ses-M156_trc-18FAV45_pet.nii.gz 1121997 +8 func/sub-001_ses-M156_task-rest_bold.json 1120325 +9 func/sub-001_ses-M156_task-rest_bold.nii.gz 1120325 diff --git a/tests/data/bids/sub-001/sub-001_sessions.tsv b/tests/data/bids/sub-001/sub-001_sessions.tsv new file mode 100644 index 0000000..d1a60c1 --- /dev/null +++ b/tests/data/bids/sub-001/sub-001_sessions.tsv @@ -0,0 +1,3 @@ +RID session_id comp_adni_mem comp_adni_ef comp_adni_lan comp_adni_vs uwnpsychsum_03_07_19_adni_mem uwnpsychsum_03_07_19_adni_ef vitals_examdate vitals_vsweight vitals_vswtunit vitals_vsheight vitals_vshtunit vitals_vsbpsys vitals_vsbpdia vitals_vspulse vitals_vsresp vitals_vstemp 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ecogpt_visspat1 ecogpt_visspat2 ecogpt_visspat3 ecogpt_visspat4 ecogpt_visspat6 ecogpt_visspat7 ecogpt_visspat8 ecogpt_plan1 ecogpt_plan2 ecogpt_plan3 ecogpt_plan4 ecogpt_plan5 ecogpt_organ1 ecogpt_organ2 ecogpt_organ3 ecogpt_organ4 ecogpt_organ5 ecogpt_organ6 ecogpt_divatt1 ecogpt_divatt2 ecogpt_divatt3 ecogpt_divatt4 ecogpt_staffasst ecogpt_validity ecogpt_source ecogpt_ecogptdivatt ecogpt_ecogptlang ecogpt_ecogptmem ecogpt_ecogptorgan ecogpt_ecogptplan ecogpt_ecogptvisspat ecogpt_ecogpttotal adas_Q1 adas_Q2 adas_Q3 adas_Q4 adas_Q5 adas_Q6 adas_Q7 adas_Q8 adas_Q9 adas_Q10 adas_Q11 adas_Q12 adas_Q13 logmem_delay logmem_imm dsst neurobat_clockcirc neurobat_clocksym neurobat_clocknum neurobat_clockhand neurobat_clocktime neurobat_clockscor neurobat_copycirc neurobat_copysym neurobat_copynum neurobat_copyhand neurobat_copytime neurobat_copyscor neurobat_lmstory neurobat_limmtotal neurobat_limmend neurobat_avtot1 neurobat_averr1 neurobat_avtot2 neurobat_averr2 neurobat_avtot3 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anart_Q4 anart_Q5 anart_Q6 anart_Q7 anart_Q8 anart_Q9 anart_Q10 anart_Q11 anart_Q12 anart_Q13 anart_Q14 anart_Q15 anart_Q16 anart_Q17 anart_Q18 anart_Q19 anart_Q20 anart_Q21 anart_Q22 anart_Q23 anart_Q24 anart_Q25 anart_Q26 anart_Q27 anart_Q28 anart_Q29 anart_Q30 anart_Q31 anart_Q32 anart_Q33 anart_Q34 anart_Q35 anart_Q36 anart_Q37 anart_Q38 anart_Q39 anart_Q40 anart_Q41 anart_Q42 anart_Q43 anart_Q44 anart_Q45 anart_Q46 anart_Q47 anart_Q48 anart_Q49 anart_Q50 cdr_global cdr_cdmemory cdr_cdorient cdr_cdjudge cdr_cdcommun cdr_cdhome cdr_cdcare cdr_cdglobal examination_date age current_study diagnosis adni_fdg adni_pib adni_av45 cdr_sb adas11 adas13 MMSE FAQ adni_ventricles_vol adni_hippocampus_vol adni_brain_vol adni_entorhinal_vol adni_icv ravlt_immediate moca adas_memory adas_language adas_concentration adas_praxis adni_fusiform_vol adni_midtemp_vol adni_abeta adni_tau adni_ptau Phase ID SITEID VISCODE VISCODE2 USERDATE USERDATE2 cci_cci1 cci_cci2 cci_cci3 cci_cci4 cci_cci5 cci_cci6 cci_cci7 cci_cci8 cci_cci9 cci_cci10 cci_cci11 cci_cci12 cci_cci13 cci_cci14 cci_cci15 cci_cci16 cci_cci17 cci_cci18 cci_cci19 cci_cci20 cci_cci12tot update_stamp PTID Timepoint CollectedDateTime bhr_longitudinal_questionnaire_latest bhr_longitudinal_questionnaire_qid49_1 bhr_longitudinal_questionnaire_qid49_2 bhr_longitudinal_questionnaire_qid49_3 bhr_longitudinal_questionnaire_qid49_4 bhr_longitudinal_questionnaire_qid49_5 bhr_everyday_cognition_qid49_6 bhr_everyday_cognition_qid49_7 bhr_everyday_cognition_qid49_8 bhr_everyday_cognition_qid50_1 bhr_everyday_cognition_qid50_2 bhr_everyday_cognition_qid50_3 bhr_everyday_cognition_qid50_4 bhr_everyday_cognition_qid50_5 bhr_longitudinal_questionnaire_qid50_6 bhr_longitudinal_questionnaire_qid50_7 bhr_longitudinal_questionnaire_qid50_8 bhr_longitudinal_questionnaire_qid50_9 bhr_everyday_cognition_qid51_1 bhr_everyday_cognition_qid51_2 bhr_everyday_cognition_qid51_3 bhr_everyday_cognition_qid51_4 bhr_everyday_cognition_qid51_5 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bhr_baseline_questionnaire_qid33_1 bhr_baseline_questionnaire_qid33_2 bhr_longitudinal_questionnaire_qid34_1 bhr_longitudinal_questionnaire_qid34_2 bhr_longitudinal_questionnaire_qid35_1 bhr_longitudinal_questionnaire_qid35_2 bhr_longitudinal_questionnaire_qid36_1 bhr_longitudinal_questionnaire_qid36_2 bhr_longitudinal_questionnaire_qid37_1 bhr_longitudinal_questionnaire_qid37_2 bhr_longitudinal_questionnaire_qid39_1 bhr_longitudinal_questionnaire_qid39_2 bhr_baseline_questionnaire_qid39_3 bhr_baseline_questionnaire_qid39_4 bhr_baseline_questionnaire_qid39_5 bhr_baseline_questionnaire_qid46_6 bhr_baseline_questionnaire_qid46_7 bhr_baseline_questionnaire_qid46_8 bhr_baseline_questionnaire_qid46_9 bhr_baseline_questionnaire_qid46_13 bhr_baseline_questionnaire_qid47_11 bhr_baseline_questionnaire_qid47_12 bhr_baseline_questionnaire_qid47_13 bhr_baseline_questionnaire_qid47_14 bhr_longitudinal_questionnaire_qid53 bhr_longitudinal_questionnaire_qid54 bhr_longitudinal_questionnaire_qid1 bhr_longitudinal_questionnaire_qid24 bhr_longitudinal_questionnaire_qid6 bhr_longitudinal_questionnaire_qid25 bhr_longitudinal_questionnaire_qid10 bhr_longitudinal_questionnaire_qid12 bhr_longitudinal_questionnaire_qid27 bhr_longitudinal_questionnaire_qid28_text bhr_longitudinal_questionnaire_qid29 bhr_longitudinal_questionnaire_qid30_text bhr_longitudinal_questionnaire_qid18_1 bhr_longitudinal_questionnaire_qid18_2 bhr_longitudinal_questionnaire_qid32_3 bhr_longitudinal_questionnaire_qid19_1 bhr_longitudinal_questionnaire_qid19_2 bhr_longitudinal_questionnaire_qid19_3 bhr_longitudinal_questionnaire_qid19_4 bhr_longitudinal_questionnaire_qid19_5 bhr_longitudinal_questionnaire_qid19_6 bhr_longitudinal_questionnaire_qid19_7 bhr_longitudinal_questionnaire_qid19_8 bhr_longitudinal_questionnaire_qid19_9 bhr_longitudinal_questionnaire_qid19_10 bhr_longitudinal_questionnaire_qid38_1 bhr_longitudinal_questionnaire_qid38_2 bhr_longitudinal_questionnaire_qid40_1 bhr_longitudinal_questionnaire_qid40_2 bhr_longitudinal_questionnaire_qid41_1 bhr_longitudinal_questionnaire_qid41_2 bhr_longitudinal_questionnaire_qid42_1 bhr_longitudinal_questionnaire_qid42_2 bhr_longitudinal_questionnaire_qid43_1 bhr_longitudinal_questionnaire_qid43_2 bhr_longitudinal_questionnaire_qid50_13 bhr_longitudinal_questionnaire_qid51_11 bhr_longitudinal_questionnaire_qid51_12 bhr_longitudinal_questionnaire_qid51_13 bhr_longitudinal_questionnaire_qid51_14 a_stat tau_stat +0074 ses-M000 0.509 0.723 1.487 0.706 0.509 0.723 04/01/2006 176.8 1 -4 -4 149 85 80 12 36.9 2 2 n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 2 0 -4 0 -4 0 -4 0 -4 0 -4 0 -4 0 -4 0 -4 0 -4 0 -4 0 -4 0 -4 0 n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 4.00 0 0 4 0 0 0 3 0 0 0 0 0 n/a n/a 42 1 1 1 1 1 5 1 1 1 1 1 5 n/a n/a n/a 5 1 5 1 7 1 9 0 11 0 6 0 5 0 n/a 9 7 6 4 24 2 0 15 0 1 24.00 0 0 100.00 3 0 42 n/a n/a n/a -4 29 0 0 1 1 29 n/a 6 2 5 1 -4 3 n/a n/a n/a n/a n/a n/a n/a 24 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 n/a n/a n/a n/a n/a n/a n/a n/a 04/01/2006 78.2 ADNI1 CN 1.29164 n/a n/a 0.0 7.0 11.0 30.0 0.0 87500.0 6444.0 1035850.0 3368.0 1712460.0 37.0 n/a 4.004030 00000 0 00 17433.0 21238.0 n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 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b/tests/data/bids/sub-002/ses-M000/anat/sub-002_ses-M000_run-01_T1w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-002/ses-M000/anat/sub-002_ses-M000_run-01_T2w.json b/tests/data/bids/sub-002/ses-M000/anat/sub-002_ses-M000_run-01_T2w.json new file mode 100644 index 0000000..57f514b --- /dev/null +++ b/tests/data/bids/sub-002/ses-M000/anat/sub-002_ses-M000_run-01_T2w.json @@ -0,0 +1,63 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.243, + "Manufacturer": "Siemens", + "ManufacturersModelName": "TrioTim", + "BodyPartExamined": "HEAD", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR B17", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI_t2", + "ProtocolName": "GENFI_t2", + "ScanningSequence": "SE", + "SequenceVariant": "SK\\SP", + "ScanOptions": "PFP", + "SequenceName": "spc3d1_282ns", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 13, + "AcquisitionTime": 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a/tests/data/bids/sub-002/ses-M000/dwi/sub-002_ses-M000_run-01_dwi.json b/tests/data/bids/sub-002/ses-M000/dwi/sub-002_ses-M000_run-01_dwi.json new file mode 100644 index 0000000..2b35777 --- /dev/null +++ b/tests/data/bids/sub-002/ses-M000/dwi/sub-002_ses-M000_run-01_dwi.json @@ -0,0 +1,132 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.243, + "Manufacturer": "Siemens", + "ManufacturersModelName": "TrioTim", + "BodyPartExamined": "HEAD", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR B17", + "MRAcquisitionType": "2D", + "SeriesDescription": "dwi_2mm_1b0_63b1000", + "ProtocolName": "dwi_2mm_1b0_63b1000", + "ScanningSequence": "EP", + "SequenceVariant": "SK\\SP", + "ScanOptions": "PFP\\FS", + "SequenceName": "ep_b0", + "ImageType": ["ORIGINAL", "PRIMARY", "DIFFUSION", "NONE", "ND", "MOSAIC"], + "SeriesNumber": 5, + "AcquisitionTime": "12:26:34.340000", + "AcquisitionNumber": 1, + "SliceThickness": 2, + "SpacingBetweenSlices": 2, + "SAR": 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b/tests/data/bids/sub-002/ses-M000/func/sub-002_ses-M000_task-rest_run-01_bold.json new file mode 100644 index 0000000..0b81e38 --- /dev/null +++ b/tests/data/bids/sub-002/ses-M000/func/sub-002_ses-M000_task-rest_run-01_bold.json @@ -0,0 +1,98 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.243, + "Manufacturer": "Siemens", + "ManufacturersModelName": "TrioTim", + "BodyPartExamined": "HEAD", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR B17", + "MRAcquisitionType": "2D", + "SeriesDescription": "rs_fMRI_3mm", + "ProtocolName": "rs_fMRI_3mm", + "ScanningSequence": "EP", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "SequenceName": "epfid2d1_64", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "MOSAIC"], + "SeriesNumber": 4, + "AcquisitionTime": "12:15:32.505000", + "AcquisitionNumber": 1, + "SliceThickness": 3, + "SpacingBetweenSlices": 3.75, + "SAR": 0.123931, + "EchoTime": 0.03, + "RepetitionTime": 2, + "FlipAngle": 78, + 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"ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0.962692, + -0.2706 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-002/ses-M000/func/sub-002_ses-M000_task-rest_run-01_bold.nii.gz b/tests/data/bids/sub-002/ses-M000/func/sub-002_ses-M000_task-rest_run-01_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-002/ses-M000/sub-002_ses-M000_scans.tsv b/tests/data/bids/sub-002/ses-M000/sub-002_ses-M000_scans.tsv new file mode 100644 index 0000000..26f6c7e --- /dev/null +++ b/tests/data/bids/sub-002/ses-M000/sub-002_ses-M000_scans.tsv @@ -0,0 +1,5 @@ +modality run_num bids_filename manufacturer number_of_parts +rsfmri run-01 sub-002_ses-M000_task-rest_run-01_bold SIEMENS 1 +T1 run-01 sub-002_ses-M000_run-01_T1w SIEMENS 1 +T2w run-01 sub-002_ses-M000_run-01_T2w SIEMENS 1 +dwi run-01 sub-002_ses-M000_run-01_dwi SIEMENS 1.0 diff --git a/tests/data/bids/sub-002/ses-M070/anat/sub-002_ses-M070_run-01_T1w.json b/tests/data/bids/sub-002/ses-M070/anat/sub-002_ses-M070_run-01_T1w.json new file mode 100644 index 0000000..64b50f2 --- /dev/null +++ b/tests/data/bids/sub-002/ses-M070/anat/sub-002_ses-M070_run-01_T1w.json @@ -0,0 +1,64 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.255, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI2_3DT1_ND", + "ProtocolName": "GENFI2_3DT1_ND", + "ScanningSequence": "GR\\IR", + "SequenceVariant": "SK\\SP\\MP\\OSP", + "ScanOptions": "IR", + "SequenceName": "*tfl3d1_16ns", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 2, + "AcquisitionTime": "15:41:26.595000", + "AcquisitionNumber": 1, + "SliceThickness": 1.1, + "SAR": 0.0558351, + "EchoTime": 0.00293, + 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b/tests/data/bids/sub-002/ses-M070/anat/sub-002_ses-M070_run-01_T1w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-002/ses-M070/anat/sub-002_ses-M070_run-01_T2w.json b/tests/data/bids/sub-002/ses-M070/anat/sub-002_ses-M070_run-01_T2w.json new file mode 100644 index 0000000..9585f8e --- /dev/null +++ b/tests/data/bids/sub-002/ses-M070/anat/sub-002_ses-M070_run-01_T2w.json @@ -0,0 +1,64 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.255, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI2_3DT2", + "ProtocolName": "GENFI2_3DT2", + "ScanningSequence": "SE", + "SequenceVariant": "SK\\SP", + "ScanOptions": "PFP\\WE", + "SequenceName": "*spc_282ns", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 4, + "AcquisitionTime": 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"ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-002/ses-M070/anat/sub-002_ses-M070_run-01_T2w.nii.gz b/tests/data/bids/sub-002/ses-M070/anat/sub-002_ses-M070_run-01_T2w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-002/ses-M070/anat/sub-002_ses-M070_run-02_T1w.json b/tests/data/bids/sub-002/ses-M070/anat/sub-002_ses-M070_run-02_T1w.json new file mode 100644 index 0000000..dae8b19 --- /dev/null +++ b/tests/data/bids/sub-002/ses-M070/anat/sub-002_ses-M070_run-02_T1w.json @@ -0,0 +1,64 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.255, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI2_3DT2", + "ProtocolName": "GENFI2_3DT2", + "ScanningSequence": "GR\\IR", + "SequenceVariant": "SK\\SP\\MP\\OSP", + 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a/tests/data/bids/sub-002/ses-M070/dwi/sub-002_ses-M070_run-02_dwi.json b/tests/data/bids/sub-002/ses-M070/dwi/sub-002_ses-M070_run-02_dwi.json new file mode 100644 index 0000000..7dcd6d7 --- /dev/null +++ b/tests/data/bids/sub-002/ses-M070/dwi/sub-002_ses-M070_run-02_dwi.json @@ -0,0 +1,130 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.255, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR E11", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_64B1000_5B0", + "ProtocolName": "GENFI2_DWI_64B1000_5B0", + "ScanningSequence": "EP", + "SequenceVariant": "SK\\SP", + "ScanOptions": "FS", + "SequenceName": "*ep_b0", + "ImageType": ["ORIGINAL", "PRIMARY", "DIFFUSION", "NONE", "ND", "MOSAIC"], + "SeriesNumber": 10, + "AcquisitionTime": "16:12:11.015000", + "AcquisitionNumber": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, 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a/tests/data/bids/sub-002/ses-M070/fmap/sub-002_ses-M070_run-01_magnitude1.json b/tests/data/bids/sub-002/ses-M070/fmap/sub-002_ses-M070_run-01_magnitude1.json new file mode 100644 index 0000000..f5eac98 --- /dev/null +++ b/tests/data/bids/sub-002/ses-M070/fmap/sub-002_ses-M070_run-01_magnitude1.json @@ -0,0 +1,118 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.255, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR E11", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_FIeldMap", + "ProtocolName": "GENFI2_FIeldMap", + "ScanningSequence": "GR", + "SequenceVariant": "SP", + "SequenceName": "*fm2d2", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], + "SeriesNumber": 7, + "AcquisitionTime": "16:01:27.390000", + "AcquisitionNumber": 1, + "SliceThickness": 3, + "SpacingBetweenSlices": 3, + "SAR": 0.095486, + "EchoNumber": 1, + 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-0,0 +1,118 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.255, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR E11", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_FIeldMap", + "ProtocolName": "GENFI2_FIeldMap", + "ScanningSequence": "GR", + "SequenceVariant": "SP", + "SequenceName": "*fm2d2", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], + "SeriesNumber": 7, + "AcquisitionTime": "16:01:28.080000", + "AcquisitionNumber": 1, + "SliceThickness": 3, + "SpacingBetweenSlices": 3, + "SAR": 0.095486, + "EchoNumber": 2, + "EchoTime": 0.00738, + "RepetitionTime": 0.688, + "FlipAngle": 60, + "PartialFourier": 1, + "BaseResolution": 64, + "ShimSetting": [ + -1490, + -11611, + -3908, + 533, + 7, + -172, + 39, + 25 ], + "TxRefAmp": 209.683, + "PhaseResolution": 1, + "ReceiveCoilName": "HeadNeck_64", + "ReceiveCoilActiveElements": 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0.989272, + -0.146083 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-002/ses-M070/fmap/sub-002_ses-M070_run-01_magnitude2.nii.gz b/tests/data/bids/sub-002/ses-M070/fmap/sub-002_ses-M070_run-01_magnitude2.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-002/ses-M070/fmap/sub-002_ses-M070_run-01_phasediff.json b/tests/data/bids/sub-002/ses-M070/fmap/sub-002_ses-M070_run-01_phasediff.json new file mode 100644 index 0000000..83cdb6a --- /dev/null +++ b/tests/data/bids/sub-002/ses-M070/fmap/sub-002_ses-M070_run-01_phasediff.json @@ -0,0 +1,120 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.255, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR E11", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_FIeldMap", + "ProtocolName": "GENFI2_FIeldMap", + "ScanningSequence": "GR", + "SequenceVariant": "SP", + "SequenceName": "*fm2d2", + "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND", "PHASE"], + "SeriesNumber": 8, + "AcquisitionTime": "16:01:28.080000", + "AcquisitionNumber": 1, + "SliceThickness": 3, + "SpacingBetweenSlices": 3, + "SAR": 0.095486, + "EchoNumber": 2, + "EchoTime": 0.00738, + "RepetitionTime": 0.688, + "FlipAngle": 60, + "EchoTime1": 0.00492, + "EchoTime2": 0.00738, + "PartialFourier": 1, + "BaseResolution": 64, + "ShimSetting": [ + -1490, + -11611, + -3908, + 533, + 7, + -172, + 39, + 25 ], + "TxRefAmp": 209.683, + "PhaseResolution": 1, + "ReceiveCoilName": "HeadNeck_64", + "ReceiveCoilActiveElements": "HC1-7;NC2", + "PulseSequenceDetails": "%SiemensSeq%\\gre_field_mapping", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingSteps": 64, + "AcquisitionMatrixPE": 64, + "ReconMatrixPE": 64, + "PixelBandwidth": 260, + "DwellTime": 3e-05, + "PhaseEncodingDirection": "i", + "SliceTiming": [ + 0, + 0.35938, + 0.01562, + 0.35938, + 0.03125, + 0.375, + 0.04688, + 0.39062, + 0.04688, + 0.40625, + 0.0625, + 0.42188, + 0.07812, + 0.42188, + 0.09375, + 0.4375, + 0.10938, + 0.45312, + 0.10938, + 0.46875, + 0.125, + 0.48438, + 0.14062, + 0.48438, + 0.15625, + 0.5, + 0.17188, + 0.51562, + 0.17188, + 0.53125, + 0.1875, + 0.54688, + 0.20312, + 0.54688, + 0.21875, + 0.5625, + 0.23438, + 0.57812, + 0.23438, + 0.59375, + 0.25, + 0.60938, + 0.26562, + 0.60938, + 0.28125, + 0.625, + 0.29688, + 0.64062, + 0.29688, + 0.65625, + 0.3125, + 0.67188, + 0.32812, + 0.67188, + 0.34375 ], + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0.989272, + -0.146083 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-002/ses-M070/fmap/sub-002_ses-M070_run-01_phasediff.nii.gz b/tests/data/bids/sub-002/ses-M070/fmap/sub-002_ses-M070_run-01_phasediff.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-002/ses-M070/func/sub-002_ses-M070_task-rest_run-01_bold.json b/tests/data/bids/sub-002/ses-M070/func/sub-002_ses-M070_task-rest_run-01_bold.json new file mode 100644 index 0000000..fff7e21 --- /dev/null +++ b/tests/data/bids/sub-002/ses-M070/func/sub-002_ses-M070_task-rest_run-01_bold.json @@ -0,0 +1,112 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.255, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR E11", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_rs_fMRI", + "ProtocolName": "GENFI2_rs_fMRI", + "ScanningSequence": "EP", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "SequenceName": "*epfid2d1_64", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "MOSAIC"], + "SeriesNumber": 5, + "AcquisitionTime": "15:52:51.727500", + "AcquisitionNumber": 1, + "SliceThickness": 3.5, + "SpacingBetweenSlices": 3.5, + "SAR": 0.077536, + "EchoTime": 0.03, + "RepetitionTime": 2.5, + "FlipAngle": 80, + "PartialFourier": 1, + "BaseResolution": 64, + "ShimSetting": [ + -1490, + -11611, + -3908, + 533, + 7, + -172, + 39, + 25 ], + "TxRefAmp": 209.683, + "PhaseResolution": 1, + "ReceiveCoilName": "HeadNeck_64", + "ReceiveCoilActiveElements": "HC1-7;NC2", + "PulseSequenceDetails": "%SiemensSeq%\\ep2d_bold", + "RefLinesPE": 24, + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 31, + "PhaseEncodingSteps": 63, + "AcquisitionMatrixPE": 64, + "ReconMatrixPE": 64, + "BandwidthPerPixelPhaseEncode": 55.804, + "ParallelReductionFactorInPlane": 2, + "EffectiveEchoSpacing": 0.000279998, + "DerivedVendorReportedEchoSpacing": 0.000559996, + "TotalReadoutTime": 0.0176399, + "PixelBandwidth": 2110, + "DwellTime": 3.7e-06, + "PhaseEncodingDirection": "j-", + "SliceTiming": [ + 1.24, + 0, + 1.3, + 0.06, + 1.36, + 0.12, + 1.4175, + 0.1775, + 1.4775, + 0.2375, + 1.535, + 0.295, + 1.595, + 0.355, + 1.655, + 0.415, + 1.7125, + 0.4725, + 1.7725, + 0.5325, + 1.83, + 0.5925, + 1.89, + 0.65, + 1.95, + 0.71, + 2.0075, + 0.7675, + 2.0675, + 0.8275, + 2.1275, + 0.8875, + 2.185, + 0.945, + 2.245, + 1.005, + 2.3025, + 1.0625, + 2.3625, + 1.1225, + 2.4225, + 1.1825 ], + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0.989272, + -0.146083 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-002/ses-M070/func/sub-002_ses-M070_task-rest_run-01_bold.nii.gz b/tests/data/bids/sub-002/ses-M070/func/sub-002_ses-M070_task-rest_run-01_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-002/ses-M070/sub-002_ses-M070_scans.tsv b/tests/data/bids/sub-002/ses-M070/sub-002_ses-M070_scans.tsv new file mode 100644 index 0000000..998f516 --- /dev/null +++ b/tests/data/bids/sub-002/ses-M070/sub-002_ses-M070_scans.tsv @@ -0,0 +1,9 @@ +modality run_num bids_filename manufacturer number_of_parts +dwi run-01 sub-002_ses-M070_run-01_dwi SIEMENS 2.0 +dwi run-02 sub-002_ses-M070_run-02_dwi SIEMENS 2.0 +T2w run-02 sub-002_ses-M070_run-02_T2w SIEMENS 1 +T2w run-01 sub-002_ses-M070_run-01_T2w SIEMENS 1 +T1 run-01 sub-002_ses-M070_run-01_T1w SIEMENS 1 +rsfmri run-01 sub-002_ses-M070_task-rest_run-01_bold SIEMENS 1 +fieldmap run-01 sub-002_ses-M070_run-01_magnitude SIEMENS 1 +fieldmap run-01 sub-002_ses-M070_run-01_phasediff SIEMENS 1 diff --git a/tests/data/bids/sub-002/sub-002_sessions.tsv b/tests/data/bids/sub-002/sub-002_sessions.tsv new file mode 100644 index 0000000..d26e907 --- /dev/null +++ b/tests/data/bids/sub-002/sub-002_sessions.tsv @@ -0,0 +1,3 @@ +session_id genfi_version +ses-M070 GENFI2 +ses-M000 GENFI1 diff --git a/tests/data/bids/sub-003/ses-M000/anat/sub-003_ses-M000_run-01_T1w.json b/tests/data/bids/sub-003/ses-M000/anat/sub-003_ses-M000_run-01_T1w.json new file mode 100644 index 0000000..1c61dc9 --- /dev/null +++ b/tests/data/bids/sub-003/ses-M000/anat/sub-003_ses-M000_run-01_T1w.json @@ -0,0 +1,59 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.198, + "Manufacturer": "Siemens", + "ManufacturersModelName": "TrioTim", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR B17", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI_t1", + "ProtocolName": "GENFI_t1", + "ScanningSequence": "GR\\IR", + "SequenceVariant": "SP\\MP", + "ScanOptions": "IR", + "SequenceName": "*tfl3d1_ns", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 2, + "AcquisitionTime": "14:58:23.370000", + "AcquisitionNumber": 1, + "SliceThickness": 1.1, + "SAR": 0.122241, + "EchoTime": 0.0029, + "RepetitionTime": 2.2, + "InversionTime": 0.9, + "FlipAngle": 10, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 6858, + -10503, + 4407, + 740, + -211, + 162, + -343, + -25 ], + "TxRefAmp": 266.517, + "PhaseResolution": 1, + "ReceiveCoilName": "32Ch_Head", + "CoilString": "C:HEA;HEP", + "PulseSequenceDetails": "%SiemensSeq%\\tfl", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingSteps": 256, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "PixelBandwidth": 238, + "DwellTime": 8.2e-06, + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-003/ses-M000/anat/sub-003_ses-M000_run-01_T1w.nii.gz b/tests/data/bids/sub-003/ses-M000/anat/sub-003_ses-M000_run-01_T1w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-003/ses-M000/anat/sub-003_ses-M000_run-01_T2w.json b/tests/data/bids/sub-003/ses-M000/anat/sub-003_ses-M000_run-01_T2w.json new file mode 100644 index 0000000..75fef8a --- /dev/null +++ b/tests/data/bids/sub-003/ses-M000/anat/sub-003_ses-M000_run-01_T2w.json @@ -0,0 +1,63 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.198, + "Manufacturer": "Siemens", + "ManufacturersModelName": "TrioTim", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR B17", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI_t2", + "ProtocolName": "GENFI_t2", + "ScanningSequence": "SE", + "SequenceVariant": "SK\\SP", + "ScanOptions": "PFP", + "SequenceName": "*spc3d1_282ns", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 3, + "AcquisitionTime": "15:08:3.180000", + "AcquisitionNumber": 1, + "SliceThickness": 1.1, + "SAR": 0.275486, + "EchoTime": 0.401, + 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+ 0.26562, + 0.60938, + 0.26562, + 0.625, + 0.28125, + 0.64062, + 0.29688, + 0.65625, + 0.3125, + 0.65625, + 0.32812, + 0.67188, + 0.32812 ], + "ImageOrientationPatientDICOM": [ + 1, + -2.05103e-10, + 0, + 2.05103e-10, + 1, + 0 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-003/ses-M000/fmap/sub-003_ses-M000_run-01_magnitude2.nii.gz b/tests/data/bids/sub-003/ses-M000/fmap/sub-003_ses-M000_run-01_magnitude2.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-003/ses-M000/fmap/sub-003_ses-M000_run-01_phasediff.json b/tests/data/bids/sub-003/ses-M000/fmap/sub-003_ses-M000_run-01_phasediff.json new file mode 100644 index 0000000..f47a613 --- /dev/null +++ b/tests/data/bids/sub-003/ses-M000/fmap/sub-003_ses-M000_run-01_phasediff.json @@ -0,0 +1,118 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.198, + "Manufacturer": "Siemens", + "ManufacturersModelName": "TrioTim", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR B17", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI_fieldmap", + "ProtocolName": "GENFI_fieldmap", + "ScanningSequence": "GR", + "SequenceVariant": "SP", + "SequenceName": "*fm2d2r", + "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND", "PHASE"], + "SeriesNumber": 13, + "AcquisitionTime": "15:25:13.232500", + "AcquisitionNumber": 1, + "SliceThickness": 3, + "SpacingBetweenSlices": 3, + "SAR": 0.212599, + "EchoNumber": 2, + "EchoTime": 0.00738, + "RepetitionTime": 0.688, + "FlipAngle": 60, + "EchoTime1": 0.00492, + "EchoTime2": 0.00738, + "PartialFourier": 1, + "BaseResolution": 64, + "ShimSetting": [ + 6853, + -10437, + 4475, + 862, + -198, + 525, + -420, + -90 ], + "TxRefAmp": 266.517, + "PhaseResolution": 1, + "ReceiveCoilName": "32Ch_Head", + "CoilString": "C:HEA;HEP", + "PulseSequenceDetails": "%SiemensSeq%\\gre_field_mapping", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingSteps": 64, + "AcquisitionMatrixPE": 64, + "ReconMatrixPE": 64, + "PixelBandwidth": 260, + "DwellTime": 3e-05, + "PhaseEncodingDirection": "i", + "SliceTiming": [ + 0, + 0.34375, + 0.01562, + 0.35938, + 0.01562, + 0.375, + 0.03125, + 0.39062, + 0.04688, + 0.39062, + 0.0625, + 0.40625, + 0.07812, + 0.42188, + 0.07812, + 0.4375, + 0.09375, + 0.45312, + 0.10938, + 0.46875, + 0.125, + 0.46875, + 0.14062, + 0.48438, + 0.14062, + 0.5, + 0.15625, + 0.51562, + 0.17188, + 0.53125, + 0.1875, + 0.53125, + 0.20312, + 0.54688, + 0.20312, + 0.5625, + 0.21875, + 0.57812, + 0.23438, + 0.59375, + 0.25, + 0.59375, + 0.26562, + 0.60938, + 0.26562, + 0.625, + 0.28125, + 0.64062, + 0.29688, + 0.65625, + 0.3125, + 0.65625, + 0.32812, + 0.67188, + 0.32812 ], + "ImageOrientationPatientDICOM": [ + 1, + -2.05103e-10, + 0, + 2.05103e-10, + 1, + 0 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-003/ses-M000/fmap/sub-003_ses-M000_run-01_phasediff.nii.gz b/tests/data/bids/sub-003/ses-M000/fmap/sub-003_ses-M000_run-01_phasediff.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-003/ses-M000/func/sub-003_ses-M000_task-rest_run-01_bold.json b/tests/data/bids/sub-003/ses-M000/func/sub-003_ses-M000_task-rest_run-01_bold.json new file mode 100644 index 0000000..e789964 --- /dev/null +++ b/tests/data/bids/sub-003/ses-M000/func/sub-003_ses-M000_task-rest_run-01_bold.json @@ -0,0 +1,101 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.198, + "Manufacturer": "Siemens", + "ManufacturersModelName": "TrioTim", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR B17", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI_rs_fMRI", + "ProtocolName": "GENFI_rs_fMRI", + "ScanningSequence": "EP", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "SequenceName": "*epfid2d1_58", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "MOSAIC"], + "SeriesNumber": 10, + "AcquisitionTime": "15:20:2.255000", + "AcquisitionNumber": 1, + "SliceThickness": 3.3, + "SpacingBetweenSlices": 3.3, + "SAR": 0.147524, + "EchoTime": 0.03, + "RepetitionTime": 2.2, + "FlipAngle": 80, + "PartialFourier": 1, + "BaseResolution": 64, + "ShimSetting": [ + 6853, + -10437, + 4475, + 862, + -198, + 525, + -420, + -90 ], + "TxRefAmp": 266.517, + "PhaseResolution": 1, + "ReceiveCoilName": "32Ch_Head", + "CoilString": "C:HEA;HEP", + "PulseSequenceDetails": "%SiemensSeq%\\ep2d_bold", + "PercentPhaseFOV": 90.625, + "PercentSampling": 100, + "PhaseEncodingSteps": 58, + "AcquisitionMatrixPE": 58, + "ReconMatrixPE": 58, + "BandwidthPerPixelPhaseEncode": 34.483, + "EffectiveEchoSpacing": 0.000499996, + "DerivedVendorReportedEchoSpacing": 0.000499996, + "TotalReadoutTime": 0.0284998, + "PixelBandwidth": 2298, + "DwellTime": 3.4e-06, + "PhaseEncodingDirection": "j-", + "SliceTiming": [ + 1.105, + 0, + 1.1675, + 0.0625, + 1.2275, + 0.125, + 1.29, + 0.185, + 1.35, + 0.2475, + 1.4125, + 0.3075, + 1.4725, + 0.37, + 1.535, + 0.43, + 1.595, + 0.4925, + 1.6575, + 0.5525, + 1.72, + 0.615, + 1.78, + 0.675, + 1.8425, + 0.7375, + 1.9025, + 0.7975, + 1.965, + 0.86, + 2.025, + 0.9225, + 2.0875, + 0.9825, + 2.1475, + 1.045 ], + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-003/ses-M000/func/sub-003_ses-M000_task-rest_run-01_bold.nii.gz b/tests/data/bids/sub-003/ses-M000/func/sub-003_ses-M000_task-rest_run-01_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-003/ses-M000/sub-003_ses-M000_scans.tsv b/tests/data/bids/sub-003/ses-M000/sub-003_ses-M000_scans.tsv new file mode 100644 index 0000000..d53be66 --- /dev/null +++ b/tests/data/bids/sub-003/ses-M000/sub-003_ses-M000_scans.tsv @@ -0,0 +1,8 @@ +modality run_num bids_filename manufacturer number_of_parts +dwi run-02 sub-003_ses-M000_run-02_dwi SIEMENS 2.0 +rsfmri run-01 sub-003_ses-M000_task-rest_run-01_bold SIEMENS 1 +T2w run-01 sub-003_ses-M000_run-01_T2w SIEMENS 1 +T1 run-01 sub-003_ses-M000_run-01_T1w SIEMENS 1 +dwi run-01 sub-003_ses-M000_run-01_dwi SIEMENS 2.0 +fieldmap run-01 sub-003_ses-M000_run-01_magnitude SIEMENS 1 +fieldmap run-01 sub-003_ses-M000_run-01_phasediff SIEMENS 1 diff --git a/tests/data/bids/sub-003/sub-003_sessions.tsv b/tests/data/bids/sub-003/sub-003_sessions.tsv new file mode 100644 index 0000000..27d72e5 --- /dev/null +++ b/tests/data/bids/sub-003/sub-003_sessions.tsv @@ -0,0 +1,2 @@ +session_id genfi_version +ses-M000 GENFI1 diff --git a/tests/data/bids/sub-004/ses-M000/anat/sub-004_ses-M000_run-01_T1w.json b/tests/data/bids/sub-004/ses-M000/anat/sub-004_ses-M000_run-01_T1w.json new file mode 100644 index 0000000..f746cbf --- /dev/null +++ b/tests/data/bids/sub-004/ses-M000/anat/sub-004_ses-M000_run-01_T1w.json @@ -0,0 +1,52 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.802, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "3.2.3\\3.2.3.2", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI_t1_axial", + "ProtocolName": "GENFI_t1_axial", + "ScanningSequence": "GR", + "SequenceVariant": "MP", + "ScanOptions": "SP", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"], + "SeriesNumber": 301, + "AcquisitionTime": "19:44:39.570000", + "AcquisitionNumber": 3, + "PhilipsRescaleSlope": 1.442, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000565606, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 1.2, + "SpacingBetweenSlices": 1.2, + "SAR": 0.022283, + "EchoTime": 0.004588, + "RepetitionTime": 0.0097625, + "FlipAngle": 8, + "CoilString": "SENSE-Head-8", + "PercentPhaseFOV": 79.1667, + "PercentSampling": 100, + "EchoTrainLength": 179, + "PhaseEncodingSteps": 192, + "AcquisitionMatrixPE": 192, + "ReconMatrixPE": 256, + "WaterFatShift": 3.07496, + "EstimatedEffectiveEchoSpacing": 2.75972e-05, + "EstimatedTotalReadoutTime": 0.00703729, + "PixelBandwidth": 141, + "PhaseEncodingAxis": "i", + "ImageOrientationPatientDICOM": [ + 0.999947, + 0.0079882, + 0.00646318, + -0.00720571, + 0.993551, + -0.113158 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M000/anat/sub-004_ses-M000_run-01_T1w.nii.gz b/tests/data/bids/sub-004/ses-M000/anat/sub-004_ses-M000_run-01_T1w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M000/anat/sub-004_ses-M000_run-02_T1w.json b/tests/data/bids/sub-004/ses-M000/anat/sub-004_ses-M000_run-02_T1w.json new file mode 100644 index 0000000..4dc4574 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M000/anat/sub-004_ses-M000_run-02_T1w.json @@ -0,0 +1,53 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.802, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "3.2.3\\3.2.3.2", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI_t1", + "ProtocolName": "GENFI_t1", + "ScanningSequence": "GR", + "SequenceVariant": "MP", + "ScanOptions": "OTHER", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"], + "SeriesNumber": 1101, + "AcquisitionTime": "20:28:15.040000", + "AcquisitionNumber": 11, + "PhilipsRescaleSlope": 4.5663, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000291867, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 1.1, + "SpacingBetweenSlices": 1.1, + "SAR": 0.0254502, + "EchoTime": 0.003047, + "RepetitionTime": 0.0066806, + "FlipAngle": 8, + "CoilString": "SENSE-Head-8", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 265, + "PhaseEncodingSteps": 256, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 1.70356, + "EstimatedEffectiveEchoSpacing": 1.53167e-05, + "EstimatedTotalReadoutTime": 0.00390576, + "PixelBandwidth": 255, + "PhaseEncodingAxis": "i", + "ImageOrientationPatientDICOM": [ + -0.00720571, + 0.996839, + -0.0791159, + 0.00732542, + -0.0790632, + -0.996843 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M000/anat/sub-004_ses-M000_run-02_T1w.nii.gz b/tests/data/bids/sub-004/ses-M000/anat/sub-004_ses-M000_run-02_T1w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M000/dwi/sub-004_ses-M000_run-01_dwi.bval b/tests/data/bids/sub-004/ses-M000/dwi/sub-004_ses-M000_run-01_dwi.bval new file mode 100644 index 0000000..0b925ca --- /dev/null +++ b/tests/data/bids/sub-004/ses-M000/dwi/sub-004_ses-M000_run-01_dwi.bval @@ -0,0 +1 @@ +0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 diff --git a/tests/data/bids/sub-004/ses-M000/dwi/sub-004_ses-M000_run-01_dwi.bvec b/tests/data/bids/sub-004/ses-M000/dwi/sub-004_ses-M000_run-01_dwi.bvec new file mode 100644 index 0000000..060e904 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M000/dwi/sub-004_ses-M000_run-01_dwi.bvec @@ -0,0 +1,3 @@ +0 0.0740899 -0.188343 0.257507 -0.703302 0.808569 0.830307 0.563488 0.0426807 -0.934389 -0.203608 -0.347536 0.710275 -0.551127 -0.924298 0.344832 -0.373926 -0.272259 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"Achieva", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "3.2.3\\3.2.3.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI_dwi_1b0_61b1000", + "ProtocolName": "GENFI_dwi_1b0_61b1000", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "SE", "M", "SE"], + "SeriesNumber": 801, + "AcquisitionTime": "20:06:31.250000", + "AcquisitionNumber": 8, + "PhilipsRescaleSlope": 3.80317, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000912239, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2, + "SpacingBetweenSlices": 2, + "SAR": 0.0688545, + "EchoTime": 0.08, + "RepetitionTime": 8.25, + "FlipAngle": 90, + "CoilString": "SENSE-Head-8", + "PercentPhaseFOV": 81.25, + "PercentSampling": 100, + "EchoTrainLength": 55, + "PartialFourierEnabled": "YES", + "PhaseEncodingStepsNoPartialFourier": 126, + "AcquisitionMatrixPE": 126, + "ReconMatrixPE": 128, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 18.9655, + "EstimatedEffectiveEchoSpacing": 0.000337535, + "EstimatedTotalReadoutTime": 0.042867, + "PixelBandwidth": 1782, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.999947, + 0.00776252, + 0.00673256, + -0.00720571, + 0.996839, + -0.0791159 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M000/dwi/sub-004_ses-M000_run-01_dwi.nii.gz b/tests/data/bids/sub-004/ses-M000/dwi/sub-004_ses-M000_run-01_dwi.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M000/func/sub-004_ses-M000_task-rest_run-01_bold.json b/tests/data/bids/sub-004/ses-M000/func/sub-004_ses-M000_task-rest_run-01_bold.json new file mode 100644 index 0000000..734b3c2 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M000/func/sub-004_ses-M000_task-rest_run-01_bold.json @@ -0,0 +1,53 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.802, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "3.2.3\\3.2.3.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI_rs_fMRI_2.75mm", + "ProtocolName": "GENFI_rs_fMRI_2.75mm", + "ScanningSequence": "GR", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"], + "SeriesNumber": 401, + "AcquisitionTime": "19:50:23.560000", + "AcquisitionNumber": 4, + "PhilipsRescaleSlope": 4.57973, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000789258, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.72, + "SpacingBetweenSlices": 2.992, + "SAR": 0.0637947, + "EchoTime": 0.03, + "RepetitionTime": 2.2, + "FlipAngle": 80, + "CoilString": "SENSE-Head-8", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 29, + "PhaseEncodingSteps": 80, + "AcquisitionMatrixPE": 80, + "ReconMatrixPE": 80, + "ParallelReductionFactorInPlane": 3, + "WaterFatShift": 12.9993, + "EstimatedEffectiveEchoSpacing": 0.000366061, + "EstimatedTotalReadoutTime": 0.0289188, + "PixelBandwidth": 1284, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.999947, + 0.0079882, + 0.00646318, + -0.00720571, + 0.993551, + -0.113158 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M000/func/sub-004_ses-M000_task-rest_run-01_bold.nii.gz b/tests/data/bids/sub-004/ses-M000/func/sub-004_ses-M000_task-rest_run-01_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M000/func/sub-004_ses-M000_task-rest_run-02_bold.json b/tests/data/bids/sub-004/ses-M000/func/sub-004_ses-M000_task-rest_run-02_bold.json new file mode 100644 index 0000000..b37670c --- /dev/null +++ b/tests/data/bids/sub-004/ses-M000/func/sub-004_ses-M000_task-rest_run-02_bold.json @@ -0,0 +1,53 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.802, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "3.2.3\\3.2.3.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "rs_fMRI_2mm", + "ProtocolName": "rs_fMRI_2mm", + "ScanningSequence": "GR", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"], + "SeriesNumber": 601, + "AcquisitionTime": "20:04:19.120000", + "AcquisitionNumber": 6, + "PhilipsRescaleSlope": 6.04518, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000924099, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2, + "SpacingBetweenSlices": 2, + "SAR": 0.0480311, + "EchoTime": 0.03, + "RepetitionTime": 2.2, + "FlipAngle": 80, + "CoilString": "SENSE-Head-8", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 110, + "AcquisitionMatrixPE": 110, + "ReconMatrixPE": 112, + "ParallelReductionFactorInPlane": 2.5, + "WaterFatShift": 12.9982, + "EstimatedEffectiveEchoSpacing": 0.000263877, + "EstimatedTotalReadoutTime": 0.0292904, + "PixelBandwidth": 2169, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.999947, + 0.0079882, + 0.00646318, + -0.00720571, + 0.993551, + -0.113158 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M000/func/sub-004_ses-M000_task-rest_run-02_bold.nii.gz b/tests/data/bids/sub-004/ses-M000/func/sub-004_ses-M000_task-rest_run-02_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M000/sub-004_ses-M000_scans.tsv b/tests/data/bids/sub-004/ses-M000/sub-004_ses-M000_scans.tsv new file mode 100644 index 0000000..c80ba38 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M000/sub-004_ses-M000_scans.tsv @@ -0,0 +1,6 @@ +modality run_num bids_filename manufacturer number_of_parts +T1 run-01 sub-004_ses-M000_run-01_T1w Philips Medical Systems 1 +rsfmri run-01 sub-004_ses-M000_task-rest_run-01_bold Philips Medical Systems 1 +T1 run-02 sub-004_ses-M000_run-02_T1w Philips Medical Systems 1 +rsfmri run-02 sub-004_ses-M000_task-rest_run-02_bold Philips Medical Systems 1 +dwi run-01 sub-004_ses-M000_run-01_dwi Philips Medical Systems 1.0 diff --git a/tests/data/bids/sub-004/ses-M017/anat/sub-004_ses-M017_run-01_T1w.json b/tests/data/bids/sub-004/ses-M017/anat/sub-004_ses-M017_run-01_T1w.json new file mode 100644 index 0000000..8413552 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M017/anat/sub-004_ses-M017_run-01_T1w.json @@ -0,0 +1,52 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI2_3DT1", + "ProtocolName": "GENFI2_3DT1", + "ScanningSequence": "GR", + "SequenceVariant": "MP", + "ScanOptions": "OTHER", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"], + "SeriesNumber": 201, + "AcquisitionTime": "13:29:40.660000", + "AcquisitionNumber": 2, + "PhilipsRescaleSlope": 4.63077, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000439714, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 1.1, + "SpacingBetweenSlices": 1.1, + "SAR": 0.0255034, + "EchoTime": 0.003103, + "RepetitionTime": 0.0067809, + "FlipAngle": 8, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 266, + "PhaseEncodingSteps": 256, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 1.70355, + "EstimatedEffectiveEchoSpacing": 1.53169e-05, + "EstimatedTotalReadoutTime": 0.00390582, + "PixelBandwidth": 255, + "PhaseEncodingAxis": "i", + "ImageOrientationPatientDICOM": [ + 0.0448878, + 0.988653, + -0.143356, + 0.0298427, + -0.144764, + -0.989016 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M017/anat/sub-004_ses-M017_run-01_T1w.nii.gz b/tests/data/bids/sub-004/ses-M017/anat/sub-004_ses-M017_run-01_T1w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M017/anat/sub-004_ses-M017_run-01_T2w.json b/tests/data/bids/sub-004/ses-M017/anat/sub-004_ses-M017_run-01_T2w.json new file mode 100644 index 0000000..52fe725 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M017/anat/sub-004_ses-M017_run-01_T2w.json @@ -0,0 +1,52 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI2_3DT2", + "ProtocolName": "GENFI2_3DT2", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "OTHER", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "SE", "M", "SE"], + "SeriesNumber": 301, + "AcquisitionTime": "13:34:40.990000", + "AcquisitionNumber": 3, + "PhilipsRescaleSlope": 3.67326, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.00015339, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 1.1, + "SpacingBetweenSlices": 1.1, + "SAR": 0.0220895, + "EchoTime": 0.248923, + "RepetitionTime": 2.2, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 78.5398, + "EchoTrainLength": 141, + "PhaseEncodingSteps": 256, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 0.371866, + "EstimatedEffectiveEchoSpacing": 3.33244e-06, + "EstimatedTotalReadoutTime": 0.000849773, + "PixelBandwidth": 1168, + "PhaseEncodingAxis": "i", + "ImageOrientationPatientDICOM": [ + 0.0448878, + 0.988653, + -0.143356, + 0.0298427, + -0.144764, + -0.989016 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M017/anat/sub-004_ses-M017_run-01_T2w.nii.gz b/tests/data/bids/sub-004/ses-M017/anat/sub-004_ses-M017_run-01_T2w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-01_dwi.bval b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-01_dwi.bval new file mode 100644 index 0000000..3ca8555 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-01_dwi.bval @@ -0,0 +1 @@ +0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 diff --git a/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-01_dwi.bvec b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-01_dwi.bvec new file mode 100644 index 0000000..bf0f793 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-01_dwi.bvec @@ -0,0 +1,3 @@ +0 0.998546 -0.0401166 -0.0246366 0.630049 -0.185272 -0.868083 0.811159 0.206567 0.940363 0.53267 0.36522 0.459044 -0.44253 -0.629273 -0.601094 -0.796944 +0 -0.0448878 -0.988653 -0.531676 0.767106 0.64615 0.348909 -0.0785389 -0.889083 -0.133977 0.787361 0.764687 0.513406 0.518547 -0.57913 0.0135898 0.582522 +0 -0.0298427 0.144764 0.84659 0.120772 0.740381 0.353122 0.579529 0.408488 0.312678 -0.310365 -0.530912 -0.725047 0.731626 0.51829 -0.799062 0.15984 diff --git a/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-01_dwi.json b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-01_dwi.json new file mode 100644 index 0000000..cbc7673 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-01_dwi.json @@ -0,0 +1,113 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_16B1000_1B0", + "ProtocolName": "GENFI2_DWI_16B1000_1B0", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "SE", "M", "SE"], + "SeriesNumber": 601, + "AcquisitionTime": "13:51:21.730000", + "AcquisitionNumber": 6, + "PhilipsRescaleSlope": 3.72063, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.00103664, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.0683792, + "EchoTime": 0.069, + "RepetitionTime": 7, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 94, + "AcquisitionMatrixPE": 94, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 13.0593, + "EstimatedEffectiveEchoSpacing": 0.00030977, + "EstimatedTotalReadoutTime": 0.0294282, + "PixelBandwidth": 3325, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.998546, + -0.0401166, + 0.0360022, + 0.0448878, + 0.988653, + -0.143356 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_16B1000_1B0", + "ProtocolName": "GENFI2_DWI_16B1000_1B0", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "SE", + "M", + "SE" + ], + "SeriesNumber": 601, + "AcquisitionTime": "13:51:21.730000", + "AcquisitionNumber": 6, + "PhilipsRescaleSlope": 3.72063, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.00103664, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.0683792, + "EchoTime": 0.069, + "RepetitionTime": 7, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 94, + "AcquisitionMatrixPE": 94, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 13.0593, + "EstimatedEffectiveEchoSpacing": 0.00030977, + "EstimatedTotalReadoutTime": 0.0294282, + "PixelBandwidth": 3325, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.998546, + -0.0401166, + 0.0360022, + 0.0448878, + 0.988653, + -0.143356 + ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317", + "MultipartID": "dwi_2" +} \ No newline at end of file diff --git a/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-01_dwi.nii.gz b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-01_dwi.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-02_dwi.bval b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-02_dwi.bval new file mode 100644 index 0000000..2efef07 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-02_dwi.bval @@ -0,0 +1 @@ +0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 diff --git a/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-02_dwi.bvec b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-02_dwi.bvec new file mode 100644 index 0000000..e1c2f31 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-02_dwi.bvec @@ -0,0 +1,3 @@ +0 0.877908 0.282966 0.145628 -0.831182 0.485802 -0.814947 0.964838 0.22202 -0.0487802 0.262089 0.803949 -0.141797 -0.200096 0.877009 -0.599045 +0 -0.0646355 0.408875 0.911348 -0.426264 -0.828567 -0.201171 0.218098 -0.70176 0.0460497 0.963648 0.589643 -0.212568 -0.811774 -0.424657 -0.317949 +0 -0.474448 -0.867612 -0.385016 -0.356981 0.278341 -0.5435 0.146702 0.676934 -0.997747 0.0518922 0.0773777 0.966803 -0.548621 0.224769 -0.734884 diff --git a/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-02_dwi.json b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-02_dwi.json new file mode 100644 index 0000000..0834f52 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-02_dwi.json @@ -0,0 +1,113 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_15B1000_1B0", + "ProtocolName": "GENFI2_DWI_15B1000_1B0", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "SE", "M", "SE"], + "SeriesNumber": 701, + "AcquisitionTime": "13:53:40.160000", + "AcquisitionNumber": 7, + "PhilipsRescaleSlope": 3.59976, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.00103843, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.0683792, + "EchoTime": 0.069, + "RepetitionTime": 7, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 94, + "AcquisitionMatrixPE": 94, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 13.0593, + "EstimatedEffectiveEchoSpacing": 0.00030977, + 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a/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-06_dwi.nii.gz b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-06_dwi.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-07_dwi.bval b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-07_dwi.bval new file mode 100644 index 0000000..2efef07 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-07_dwi.bval @@ -0,0 +1 @@ +0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 diff --git a/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-07_dwi.bvec b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-07_dwi.bvec new file mode 100644 index 0000000..ce9bc17 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-07_dwi.bvec @@ -0,0 +1,3 @@ +0 -0.353107 -0.33109 -0.292781 -0.949596 -0.959384 0.490455 -0.79403 0.712348 -0.666772 0.641302 -0.0884407 -0.734914 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b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-09_dwi.json @@ -0,0 +1,113 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_1B0", + "ProtocolName": "GENFI2_DWI_1B0", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "SE", "M", "SE"], + "SeriesNumber": 1401, + "AcquisitionTime": "14:10:40.450000", + "AcquisitionNumber": 14, + "PhilipsRescaleSlope": 3.47106, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.00100743, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.0683718, + "EchoTime": 0.069, + "RepetitionTime": 7, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + 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"InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317", + "MultipartID": "dwi_1" +} \ No newline at end of file diff --git a/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-09_dwi.nii.gz b/tests/data/bids/sub-004/ses-M017/dwi/sub-004_ses-M017_run-09_dwi.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M017/fmap/sub-004_ses-M017_run-01_magnitude1.json b/tests/data/bids/sub-004/ses-M017/fmap/sub-004_ses-M017_run-01_magnitude1.json new file mode 100644 index 0000000..15e5271 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M017/fmap/sub-004_ses-M017_run-01_magnitude1.json @@ -0,0 +1,51 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_FIeldMap", + "ProtocolName": "GENFI2_FIeldMap", + "ScanningSequence": "GR", + "SequenceVariant": "SS", + "ScanOptions": "FC", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"], + "SeriesNumber": 501, + "AcquisitionTime": "13:49:14.000000", + "AcquisitionNumber": 5, + "PhilipsRescaleSlope": 1.2591, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000982909, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 3, + "SpacingBetweenSlices": 4, + "SAR": 0.139658, + "EchoNumber": 1, + "EchoTime": 0.004603, + "RepetitionTime": 0.688001, + "FlipAngle": 60, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingSteps": 64, + "AcquisitionMatrixPE": 64, + "ReconMatrixPE": 64, + "WaterFatShift": 1.5184, + "EstimatedEffectiveEchoSpacing": 2.77333e-05, + "EstimatedTotalReadoutTime": 0.0017472, + "PixelBandwidth": 286, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.998546, + -0.0401166, + 0.0360022, + 0.0448878, + 0.988653, + -0.143356 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M017/fmap/sub-004_ses-M017_run-01_magnitude1.nii.gz b/tests/data/bids/sub-004/ses-M017/fmap/sub-004_ses-M017_run-01_magnitude1.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M017/func/sub-004_ses-M017_task-rest_run-01_bold.json b/tests/data/bids/sub-004/ses-M017/func/sub-004_ses-M017_task-rest_run-01_bold.json new file mode 100644 index 0000000..fe3cca0 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M017/func/sub-004_ses-M017_task-rest_run-01_bold.json @@ -0,0 +1,51 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_rs_fMRI", + "ProtocolName": "GENFI2_rs_fMRI", + "ScanningSequence": "GR", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"], + "SeriesNumber": 401, + "AcquisitionTime": "13:40:33.250000", + "AcquisitionNumber": 4, + "PhilipsRescaleSlope": 0.819048, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.00260522, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 3.5, + "SpacingBetweenSlices": 3.5, + "SAR": 0.0660081, + "EchoTime": 0.03, + "RepetitionTime": 2.5, + "FlipAngle": 80, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 63, + "PhaseEncodingSteps": 63, + "AcquisitionMatrixPE": 63, + "ReconMatrixPE": 64, + "WaterFatShift": 15.5678, + "EstimatedEffectiveEchoSpacing": 0.0005598, + "EstimatedTotalReadoutTime": 0.0352674, + "PixelBandwidth": 2515, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.998546, + -0.0401166, + 0.0360022, + 0.0448878, + 0.988653, + -0.143356 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M017/func/sub-004_ses-M017_task-rest_run-01_bold.nii.gz b/tests/data/bids/sub-004/ses-M017/func/sub-004_ses-M017_task-rest_run-01_bold.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M017/sub-004_ses-M017_scans.tsv b/tests/data/bids/sub-004/ses-M017/sub-004_ses-M017_scans.tsv new file mode 100644 index 0000000..be32328 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M017/sub-004_ses-M017_scans.tsv @@ -0,0 +1,13 @@ +modality run_num bids_filename manufacturer number_of_parts +dwi run-02 sub-004_ses-M017_run-02_dwi Philips Medical Systems 9.0 +dwi run-07 sub-004_ses-M017_run-07_dwi Philips Medical Systems 9.0 +dwi run-04 sub-004_ses-M017_run-04_dwi Philips Medical Systems 9.0 +T2w run-01 sub-004_ses-M017_run-01_T2w Philips Medical Systems 1 +rsfmri run-01 sub-004_ses-M017_task-rest_run-01_bold Philips Medical Systems 1 +dwi run-06 sub-004_ses-M017_run-06_dwi Philips Medical Systems 9.0 +dwi run-05 sub-004_ses-M017_run-05_dwi Philips Medical Systems 9.0 +dwi run-09 sub-004_ses-M017_run-09_dwi Philips Medical Systems 9.0 +dwi run-08 sub-004_ses-M017_run-08_dwi Philips Medical Systems 9.0 +dwi run-01 sub-004_ses-M017_run-01_dwi Philips Medical Systems 9.0 +T1 run-01 sub-004_ses-M017_run-01_T1w Philips Medical Systems 1 +dwi run-03 sub-004_ses-M017_run-03_dwi Philips Medical Systems 9.0 diff --git a/tests/data/bids/sub-004/ses-M027/anat/sub-004_ses-M027_run-01_T1w.json b/tests/data/bids/sub-004/ses-M027/anat/sub-004_ses-M027_run-01_T1w.json new file mode 100644 index 0000000..fc996fd --- /dev/null +++ b/tests/data/bids/sub-004/ses-M027/anat/sub-004_ses-M027_run-01_T1w.json @@ -0,0 +1,51 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI2_3DT1_AXIAL", + "ProtocolName": "GENFI2_3DT1_AXIAL", + "ScanningSequence": "GR", + "SequenceVariant": "MP", + "ScanOptions": "SP", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"], + "SeriesNumber": 1101, + "AcquisitionTime": "13:54:8.010000", + "AcquisitionNumber": 11, + "PhilipsRescaleSlope": 2.29353, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000734099, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 1.2, + "SpacingBetweenSlices": 1.2, + "SAR": 0.0223021, + "EchoTime": 0.004589, + "RepetitionTime": 0.0097441, + "FlipAngle": 8, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 79.1667, + "PercentSampling": 100, + "EchoTrainLength": 179, + "PhaseEncodingSteps": 192, + "AcquisitionMatrixPE": 192, + "ReconMatrixPE": 256, + "WaterFatShift": 3.03207, + "EstimatedEffectiveEchoSpacing": 2.72123e-05, + "EstimatedTotalReadoutTime": 0.00693914, + "PixelBandwidth": 143, + "PhaseEncodingAxis": "i", + "ImageOrientationPatientDICOM": [ + 0.99822, + 0.0562799, + -0.0197335, + -0.0586451, + 0.986453, + -0.153202 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M027/anat/sub-004_ses-M027_run-01_T1w.nii.gz b/tests/data/bids/sub-004/ses-M027/anat/sub-004_ses-M027_run-01_T1w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M027/sub-004_ses-M027_scans.tsv b/tests/data/bids/sub-004/ses-M027/sub-004_ses-M027_scans.tsv new file mode 100644 index 0000000..13d4dda --- /dev/null +++ b/tests/data/bids/sub-004/ses-M027/sub-004_ses-M027_scans.tsv @@ -0,0 +1,2 @@ +modality run_num bids_filename manufacturer number_of_parts +T1 run-01 sub-004_ses-M027_run-01_T1w Philips Medical Systems 1 diff --git a/tests/data/bids/sub-004/ses-M039/anat/sub-004_ses-M039_run-01_T1w.json b/tests/data/bids/sub-004/ses-M039/anat/sub-004_ses-M039_run-01_T1w.json new file mode 100644 index 0000000..d517377 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/anat/sub-004_ses-M039_run-01_T1w.json @@ -0,0 +1,52 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI2_3DT1", + "ProtocolName": "GENFI2_3DT1", + "ScanningSequence": "GR", + "SequenceVariant": "MP", + "ScanOptions": "OTHER", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"], + "SeriesNumber": 1001, + "AcquisitionTime": "12:47:26.890000", + "AcquisitionNumber": 10, + "PhilipsRescaleSlope": 4.13602, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000353937, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 1.1, + "SpacingBetweenSlices": 1.1, + "SAR": 0.0254503, + "EchoTime": 0.003083, + "RepetitionTime": 0.0067424, + "FlipAngle": 8, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 265, + "PhaseEncodingSteps": 256, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 1.70355, + "EstimatedEffectiveEchoSpacing": 1.53167e-05, + "EstimatedTotalReadoutTime": 0.00390576, + "PixelBandwidth": 255, + "PhaseEncodingAxis": "i", + "ImageOrientationPatientDICOM": [ + 0.0240944, + 0.992256, + -0.121853, + -0.0279044, + -0.121173, + -0.992239 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M039/anat/sub-004_ses-M039_run-01_T1w.nii.gz b/tests/data/bids/sub-004/ses-M039/anat/sub-004_ses-M039_run-01_T1w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M039/anat/sub-004_ses-M039_run-01_T2w.json b/tests/data/bids/sub-004/ses-M039/anat/sub-004_ses-M039_run-01_T2w.json new file mode 100644 index 0000000..3ec69a0 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/anat/sub-004_ses-M039_run-01_T2w.json @@ -0,0 +1,52 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI2_3DT2", + "ProtocolName": "GENFI2_3DT2", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "OTHER", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "SE", "M", "SE"], + "SeriesNumber": 901, + "AcquisitionTime": "12:42:35.930000", + "AcquisitionNumber": 9, + "PhilipsRescaleSlope": 3.86007, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000117815, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 1.1, + "SpacingBetweenSlices": 1.1, + "SAR": 0.0220895, + "EchoTime": 0.245409, + "RepetitionTime": 2.2, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 78.5398, + "EchoTrainLength": 141, + "PhaseEncodingSteps": 256, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 0.355961, + "EstimatedEffectiveEchoSpacing": 3.18992e-06, + "EstimatedTotalReadoutTime": 0.00081343, + "PixelBandwidth": 1221, + "PhaseEncodingAxis": "i", + "ImageOrientationPatientDICOM": [ + 0.0240944, + 0.992256, + -0.121853, + -0.0279044, + -0.121173, + -0.992239 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M039/anat/sub-004_ses-M039_run-01_T2w.nii.gz b/tests/data/bids/sub-004/ses-M039/anat/sub-004_ses-M039_run-01_T2w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-01_dwi.bval b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-01_dwi.bval new file mode 100644 index 0000000..3ca8555 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-01_dwi.bval @@ -0,0 +1 @@ +0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-01_dwi.bvec b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-01_dwi.bvec new file mode 100644 index 0000000..dd1cda7 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-01_dwi.bvec @@ -0,0 +1,3 @@ +0 0.999323 -0.0272491 -0.0624533 0.605345 -0.241874 -0.894451 0.777552 0.201473 0.923228 0.532812 0.379007 0.489342 -0.495388 -0.645799 -0.553721 -0.817213 +0 -0.0235719 -0.990077 -0.536821 0.779582 0.637919 0.328468 -0.0646012 -0.886789 -0.115793 0.800189 0.775214 0.527069 0.50495 -0.59522 0.00534622 0.564615 +0 0.0282366 0.137858 0.841382 0.160654 0.731134 0.303425 0.625492 0.415949 0.36639 -0.275334 -0.505367 -0.694797 0.706836 0.47818 -0.832685 0.115642 diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-01_dwi.json b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-01_dwi.json new file mode 100644 index 0000000..ee637f5 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-01_dwi.json @@ -0,0 +1,113 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_16B1000_1B0", + "ProtocolName": "GENFI2_DWI_16B1000_1B0", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "SE", "M", "SE"], + "SeriesNumber": 1101, + "AcquisitionTime": "12:54:30.280000", + "AcquisitionNumber": 11, + "PhilipsRescaleSlope": 2.93919, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000805815, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.0683754, + "EchoTime": 0.069, + "RepetitionTime": 7, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 94, + "AcquisitionMatrixPE": 94, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 13.0593, + "EstimatedEffectiveEchoSpacing": 0.00030977, + "EstimatedTotalReadoutTime": 0.0294282, + "PixelBandwidth": 3325, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.999323, + -0.0272491, + -0.0247068, + 0.0235719, + 0.990077, + -0.138534 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_16B1000_1B0", + "ProtocolName": "GENFI2_DWI_16B1000_1B0", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "SE", + "M", + "SE" + ], + "SeriesNumber": 1101, + "AcquisitionTime": "12:54:30.280000", + "AcquisitionNumber": 11, + "PhilipsRescaleSlope": 2.93919, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000805815, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.0683754, + "EchoTime": 0.069, + "RepetitionTime": 7, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 94, + "AcquisitionMatrixPE": 94, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 13.0593, + "EstimatedEffectiveEchoSpacing": 0.00030977, + "EstimatedTotalReadoutTime": 0.0294282, + "PixelBandwidth": 3325, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.999323, + -0.0272491, + -0.0247068, + 0.0235719, + 0.990077, + -0.138534 + ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317", + "MultipartID": "dwi_1" +} \ No newline at end of file diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-01_dwi.nii.gz b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-01_dwi.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-02_dwi.bval b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-02_dwi.bval new file mode 100644 index 0000000..2efef07 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-02_dwi.bval @@ -0,0 +1 @@ +0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-02_dwi.bvec b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-02_dwi.bvec new file mode 100644 index 0000000..0d91572 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-02_dwi.bvec @@ -0,0 +1,3 @@ +0 0.905218 0.324144 0.1482 -0.799657 0.486446 -0.777427 0.949761 0.197252 0.008397 0.237885 0.785244 -0.193233 -0.150359 0.871351 -0.548296 +0 -0.0433737 0.419636 0.916373 -0.441753 -0.819646 -0.215324 0.237646 -0.700691 0.050605 0.968673 0.606086 -0.220944 -0.812736 -0.407252 -0.32643 +0 -0.422728 -0.847842 -0.371884 -0.406698 0.302572 -0.590968 0.203663 0.685656 -0.998683 0.0712955 0.126699 0.955952 -0.562896 0.273667 -0.769945 diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-02_dwi.json b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-02_dwi.json new file mode 100644 index 0000000..60e5898 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-02_dwi.json @@ -0,0 +1,113 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_15B1000_1B0", + "ProtocolName": "GENFI2_DWI_15B1000_1B0", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "SE", "M", "SE"], + "SeriesNumber": 1201, + "AcquisitionTime": "12:56:49.170000", + "AcquisitionNumber": 12, + "PhilipsRescaleSlope": 2.89719, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000807213, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.0683754, + "EchoTime": 0.069, + "RepetitionTime": 7, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 94, + "AcquisitionMatrixPE": 94, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 13.0593, + "EstimatedEffectiveEchoSpacing": 0.00030977, + "EstimatedTotalReadoutTime": 0.0294282, + "PixelBandwidth": 3325, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.999323, + -0.0272491, + -0.0247068, + 0.0235719, + 0.990077, + -0.138534 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_15B1000_1B0", + "ProtocolName": "GENFI2_DWI_15B1000_1B0", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "SE", + "M", + "SE" + ], + "SeriesNumber": 1201, + "AcquisitionTime": "12:56:49.170000", + "AcquisitionNumber": 12, + "PhilipsRescaleSlope": 2.89719, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000807213, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.0683754, + "EchoTime": 0.069, + "RepetitionTime": 7, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 94, + "AcquisitionMatrixPE": 94, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 13.0593, + "EstimatedEffectiveEchoSpacing": 0.00030977, + "EstimatedTotalReadoutTime": 0.0294282, + "PixelBandwidth": 3325, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.999323, + -0.0272491, + -0.0247068, + 0.0235719, + 0.990077, + -0.138534 + ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317", + "MultipartID": "dwi_1" +} \ No newline at end of file diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-02_dwi.nii.gz b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-02_dwi.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-03_dwi.bval b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-03_dwi.bval new file mode 100644 index 0000000..2efef07 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-03_dwi.bval @@ -0,0 +1 @@ +0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-03_dwi.bvec b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-03_dwi.bvec new file mode 100644 index 0000000..184abac --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-03_dwi.bvec @@ -0,0 +1,3 @@ +0 -0.407024 -0.277369 -0.351428 -0.956427 -0.969213 0.475241 -0.791891 0.683233 -0.710758 0.679336 -0.138796 -0.76383 -0.139172 0.586269 -0.101989 +0 -0.0059551 0.0752631 0.265968 0.291274 -0.153697 0.878832 -0.591471 -0.341012 0.0924196 -0.609588 0.814499 -0.290728 -0.733876 0.652694 0.463709 +0 0.913398 -0.957811 0.897641 -0.0201818 0.192361 -0.042428 0.151888 0.64568 0.697339 -0.40854 0.563318 0.57623 0.664874 0.479874 0.880098 diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-03_dwi.json b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-03_dwi.json new file mode 100644 index 0000000..025c8af --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-03_dwi.json @@ -0,0 +1,113 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_15B1000_1B0", + "ProtocolName": "GENFI2_DWI_15B1000_1B0", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "SE", "M", "SE"], + "SeriesNumber": 1301, + "AcquisitionTime": "12:59:13.100000", + "AcquisitionNumber": 13, + "PhilipsRescaleSlope": 2.92943, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000807213, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.0683754, + "EchoTime": 0.069, + "RepetitionTime": 7, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 94, + "AcquisitionMatrixPE": 94, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 13.0593, + "EstimatedEffectiveEchoSpacing": 0.00030977, + "EstimatedTotalReadoutTime": 0.0294282, + "PixelBandwidth": 3325, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.999323, + -0.0272491, + -0.0247068, + 0.0235719, + 0.990077, + -0.138534 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_15B1000_1B0", + "ProtocolName": "GENFI2_DWI_15B1000_1B0", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "SE", + "M", + "SE" + ], + "SeriesNumber": 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+ "MultipartID": "dwi_1" +} \ No newline at end of file diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-03_dwi.nii.gz b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-03_dwi.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-04_dwi.bval b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-04_dwi.bval new file mode 100644 index 0000000..612ac5a --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-04_dwi.bval @@ -0,0 +1 @@ +0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-04_dwi.bvec b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-04_dwi.bvec new file mode 100644 index 0000000..6445098 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-04_dwi.bvec @@ -0,0 +1,3 @@ +0 -0.536763 0.857384 0.359655 -0.170688 -0.701793 0.42877 0.470072 -0.136081 0.43192 0.395816 -0.722101 0.245184 0.0235345 0.0509311 0.597051 -0.262418 0.695841 0.242772 +0 0.83339 0.392755 0.649938 -0.505887 0.704304 -0.767246 -0.622989 0.390915 -0.321815 0.853504 0.352253 -0.935677 -0.214385 0.951821 0.180996 -0.268383 -0.573072 -0.968482 +0 0.131708 -0.33262 0.6695 -0.845543 -0.106973 -0.476959 0.625234 -0.910312 0.842544 0.338911 0.595389 -0.253757 -0.976466 0.302396 -0.781518 -0.92688 0.43289 0.0557171 diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-04_dwi.json b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-04_dwi.json new file mode 100644 index 0000000..37ae1d9 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-04_dwi.json @@ -0,0 +1,113 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_18B1000_1B0", + "ProtocolName": "GENFI2_DWI_18B1000_1B0", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "SE", "M", "SE"], + "SeriesNumber": 1401, + "AcquisitionTime": "13:01:24.610000", + "AcquisitionNumber": 14, + "PhilipsRescaleSlope": 2.84933, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000803456, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.0683754, + "EchoTime": 0.069, + "RepetitionTime": 7, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 94, + "AcquisitionMatrixPE": 94, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 13.0593, + "EstimatedEffectiveEchoSpacing": 0.00030977, + "EstimatedTotalReadoutTime": 0.0294282, + "PixelBandwidth": 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"UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.0683754, + "EchoTime": 0.069, + "RepetitionTime": 7, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 94, + "AcquisitionMatrixPE": 94, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 13.0593, + "EstimatedEffectiveEchoSpacing": 0.00030977, + "EstimatedTotalReadoutTime": 0.0294282, + "PixelBandwidth": 3325, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.999323, + -0.0272491, + -0.0247068, + 0.0235719, + 0.990077, + -0.138534 + ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317", + "MultipartID": "dwi_1" +} \ No newline at end of file diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-04_dwi.nii.gz b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-04_dwi.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-05_dwi.json b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-05_dwi.json new file mode 100644 index 0000000..a425e81 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-05_dwi.json @@ -0,0 +1,113 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_1B0", + "ProtocolName": "GENFI2_DWI_1B0", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "SE", "M", "SE"], + "SeriesNumber": 1501, + "AcquisitionTime": "13:04:10.630000", + "AcquisitionNumber": 15, + "PhilipsRescaleSlope": 2.90159, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000783112, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.0683718, + "EchoTime": 0.069, + "RepetitionTime": 7, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 94, + "AcquisitionMatrixPE": 94, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 13.0593, + "EstimatedEffectiveEchoSpacing": 0.00030977, + "EstimatedTotalReadoutTime": 0.0294281, + "PixelBandwidth": 3325, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.999323, + -0.0272491, + -0.0247068, + 0.0235719, + 0.990077, + -0.138534 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_1B0", + "ProtocolName": "GENFI2_DWI_1B0", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "FS", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "SE", + "M", + "SE" + ], + "SeriesNumber": 1501, + "AcquisitionTime": "13:04:10.630000", + "AcquisitionNumber": 15, + "PhilipsRescaleSlope": 2.90159, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000783112, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.0683718, + "EchoTime": 0.069, + "RepetitionTime": 7, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 94, + "AcquisitionMatrixPE": 94, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 13.0593, + "EstimatedEffectiveEchoSpacing": 0.00030977, + "EstimatedTotalReadoutTime": 0.0294281, + "PixelBandwidth": 3325, + "PhaseEncodingAxis": "j", + "ImageOrientationPatientDICOM": [ + 0.999323, + -0.0272491, + -0.0247068, + 0.0235719, + 0.990077, + -0.138534 + ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317", + "MultipartID": "dwi_1" +} \ No newline at end of file diff --git a/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-05_dwi.nii.gz b/tests/data/bids/sub-004/ses-M039/dwi/sub-004_ses-M039_run-05_dwi.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M039/sub-004_ses-M039_scans.tsv b/tests/data/bids/sub-004/ses-M039/sub-004_ses-M039_scans.tsv new file mode 100644 index 0000000..75616a0 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M039/sub-004_ses-M039_scans.tsv @@ -0,0 +1,8 @@ +modality run_num bids_filename manufacturer number_of_parts +dwi run-02 sub-004_ses-M039_run-02_dwi Philips Medical Systems 5.0 +T2w run-01 sub-004_ses-M039_run-01_T2w Philips Medical Systems 1 +dwi run-01 sub-004_ses-M039_run-01_dwi Philips Medical Systems 5.0 +dwi run-05 sub-004_ses-M039_run-05_dwi Philips Medical Systems 5.0 +T1 run-01 sub-004_ses-M039_run-01_T1w Philips Medical Systems 1 +dwi run-04 sub-004_ses-M039_run-04_dwi Philips Medical Systems 5.0 +dwi run-03 sub-004_ses-M039_run-03_dwi Philips Medical Systems 5.0 diff --git a/tests/data/bids/sub-004/ses-M050/anat/sub-004_ses-M050_run-01_T1w.json b/tests/data/bids/sub-004/ses-M050/anat/sub-004_ses-M050_run-01_T1w.json new file mode 100644 index 0000000..1f422bc --- /dev/null +++ b/tests/data/bids/sub-004/ses-M050/anat/sub-004_ses-M050_run-01_T1w.json @@ -0,0 +1,52 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI2_3DT1", + "ProtocolName": "GENFI2_3DT1", + "ScanningSequence": "GR", + "SequenceVariant": "MP", + "ScanOptions": "OTHER", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"], + "SeriesNumber": 1001, + "AcquisitionTime": "13:10:13.180000", + "AcquisitionNumber": 10, + "PhilipsRescaleSlope": 4.42198, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000344956, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 1.1, + "SpacingBetweenSlices": 1.1, + "SAR": 0.0254503, + "EchoTime": 0.003126, + "RepetitionTime": 0.0067907, + "FlipAngle": 8, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 265, + "PhaseEncodingSteps": 256, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 1.70355, + "EstimatedEffectiveEchoSpacing": 1.53167e-05, + "EstimatedTotalReadoutTime": 0.00390576, + "PixelBandwidth": 255, + "PhaseEncodingAxis": "i", + "ImageOrientationPatientDICOM": [ + -0.0212778, + 0.979278, + -0.201402, + -0.0229139, + -0.201872, + -0.979144 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M050/anat/sub-004_ses-M050_run-01_T1w.nii.gz b/tests/data/bids/sub-004/ses-M050/anat/sub-004_ses-M050_run-01_T1w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M050/anat/sub-004_ses-M050_run-01_T2w.json b/tests/data/bids/sub-004/ses-M050/anat/sub-004_ses-M050_run-01_T2w.json new file mode 100644 index 0000000..8ee86fc --- /dev/null +++ b/tests/data/bids/sub-004/ses-M050/anat/sub-004_ses-M050_run-01_T2w.json @@ -0,0 +1,52 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.801, + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "PatientPosition": "HFS", + "SoftwareVersions": "5.1.7\\5.1.7.2", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI2_3DT2", + "ProtocolName": "GENFI2_3DT2", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "OTHER", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "SE", "M", "SE"], + "SeriesNumber": 901, + "AcquisitionTime": "13:05:21.140000", + "AcquisitionNumber": 9, + "PhilipsRescaleSlope": 3.84054, + "PhilipsRescaleIntercept": 0, + "PhilipsScaleSlope": 0.000115537, + "UsePhilipsFloatNotDisplayScaling": 1, + "SliceThickness": 1.1, + "SpacingBetweenSlices": 1.1, + "SAR": 0.0220895, + "EchoTime": 0.248923, + "RepetitionTime": 2.2, + "FlipAngle": 90, + "CoilString": "MULTI COIL", + "PercentPhaseFOV": 100, + "PercentSampling": 78.5398, + "EchoTrainLength": 141, + "PhaseEncodingSteps": 256, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "WaterFatShift": 0.362349, + "EstimatedEffectiveEchoSpacing": 3.24716e-06, + "EstimatedTotalReadoutTime": 0.000828027, + "PixelBandwidth": 1199, + "PhaseEncodingAxis": "i", + "ImageOrientationPatientDICOM": [ + -0.0212778, + 0.979278, + -0.201402, + -0.0229139, + -0.201872, + -0.979144 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M050/anat/sub-004_ses-M050_run-01_T2w.nii.gz b/tests/data/bids/sub-004/ses-M050/anat/sub-004_ses-M050_run-01_T2w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M050/sub-004_ses-M050_scans.tsv b/tests/data/bids/sub-004/ses-M050/sub-004_ses-M050_scans.tsv new file mode 100644 index 0000000..bc8a20a --- /dev/null +++ b/tests/data/bids/sub-004/ses-M050/sub-004_ses-M050_scans.tsv @@ -0,0 +1,3 @@ +modality run_num bids_filename manufacturer number_of_parts +T2w run-01 sub-004_ses-M050_run-01_T2w Philips Medical Systems 1 +T1 run-01 sub-004_ses-M050_run-01_T1w Philips Medical Systems 1 diff --git a/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-01_T1w.json b/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-01_T1w.json new file mode 100644 index 0000000..bfe3c53 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-01_T1w.json @@ -0,0 +1,44 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.758, + "Manufacturer": "GE", + "ManufacturersModelName": "SIGNA Premier", + "BodyPartExamined": "HEAD", + "PatientPosition": "HFS", + "SoftwareVersions": "27\\LX\\MR Software release:RX27.0_R02_1831.a", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI2_3DT1", + "ProtocolName": "GENFI2_3DT1", + "ScanningSequence": "GR\\IR", + "SequenceVariant": "SS\\SP\\SK", + "ScanOptions": "FAST_GEMS\\EDR_GEMS\\FILTERED_GEMS\\ACC_GEMS\\IR_GEMS", + "ImageType": ["ORIGINAL", "PRIMARY", "OTHER"], + "SeriesNumber": 5, + "AcquisitionTime": "15:00:50.000000", + "AcquisitionNumber": 1, + "SliceThickness": 1.1, + "SpacingBetweenSlices": 1.1, + "SAR": 0.106324, + "EchoTime": 0.002892, + "RepetitionTime": 0.007164, + "InversionTime": 0.4, + "FlipAngle": 8, + "CoilString": "48HAP", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "PixelBandwidth": 244.141, + "ImageOrientationPatientDICOM": [ + -0, + 1, + 0, + -0, + -0, + -1 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-01_T1w.nii.gz b/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-01_T1w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-01_T2w.json b/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-01_T2w.json new file mode 100644 index 0000000..b984d8b --- /dev/null +++ b/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-01_T2w.json @@ -0,0 +1,45 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.758, + "Manufacturer": "GE", + "ManufacturersModelName": "SIGNA Premier", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "27\\LX\\MR Software release:RX27.0_R02_1831.a", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI2_3DT2", + "ProtocolName": "GENFI2_3DT2", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "EDR_GEMS\\HYPERSENSE_GEMS\\FILTERED_GEMS\\ACC_GEMS\\FR_GEMS", + "ImageType": ["ORIGINAL", "PRIMARY", "OTHER"], + "SeriesNumber": 6, + "AcquisitionTime": "15:10:13.000000", + "AcquisitionNumber": 1, + "SliceThickness": 1.1, + "SpacingBetweenSlices": 1.1, + "SAR": 0.3161, + "EchoTime": 0.091599, + "RepetitionTime": 3.202, + "FlipAngle": 90, + "CoilString": "48HAP", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 140, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "PixelBandwidth": 781.25, + "PhaseEncodingAxis": "i", + "ImageOrientationPatientDICOM": [ + -0, + 1, + 0, + -0, + -0, + -1 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-01_T2w.nii.gz b/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-01_T2w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-02_T2w.json b/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-02_T2w.json new file mode 100644 index 0000000..166adc3 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-02_T2w.json @@ -0,0 +1,45 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.758, + "Manufacturer": "GE", + "ManufacturersModelName": "SIGNA Premier", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "27\\LX\\MR Software release:RX27.0_R02_1831.a", + "MRAcquisitionType": "3D", + "SeriesDescription": "GENFI2_3DT2", + "ProtocolName": "GENFI2_3DT2", + "ScanningSequence": "SE", + "SequenceVariant": "SK", + "ScanOptions": "EDR_GEMS\\HYPERSENSE_GEMS\\ACC_GEMS\\FR_GEMS", + "ImageType": ["ORIGINAL", "PRIMARY", "OTHER"], + "SeriesNumber": 40006, + "AcquisitionTime": "15:10:13.000000", + "AcquisitionNumber": 1, + "SliceThickness": 1.1, + "SpacingBetweenSlices": 1.1, + "SAR": 0.3161, + "EchoTime": 0.091599, + "RepetitionTime": 3.202, + "FlipAngle": 90, + "CoilString": "48HAP", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 140, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "PixelBandwidth": 781.25, + "PhaseEncodingAxis": "i", + "ImageOrientationPatientDICOM": [ + -0, + 1, + 0, + -0, + -0, + -1 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-02_T2w.nii.gz b/tests/data/bids/sub-004/ses-M063/anat/sub-004_ses-M063_run-02_T2w.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-01_dwi.bval b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-01_dwi.bval new file mode 100644 index 0000000..fa2b605 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-01_dwi.bval @@ -0,0 +1 @@ +0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 diff --git a/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-01_dwi.bvec b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-01_dwi.bvec new file mode 100644 index 0000000..06205ab --- /dev/null +++ b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-01_dwi.bvec @@ -0,0 +1,3 @@ +0 0 -1 0.422 0.209 -0.8 0.049 0.669 -0.444 0.266 -0.802 0.055 0.357 -0.136 0.296 0.668 0.186 0.742 -0.517 -0.319 0.074 0.817 -0.301 0.628 -0.978 -0.224 0.013 -0.153 -0.598 0.042 0.051 -0.924 0.161 0.238 0.403 0.353 0.841 0.959 -0.858 0.563 -0.933 0.543 -0.672 -0.415 0.363 0.091 -0.586 0.121 0.43 -0.85 -0.329 0.171 0.44 -0.42 -0.607 0.043 -0.26 -0.094 0.682 -0.276 -0.101 0.159 -0.493 +0 0 0 0.907 0.512 -0.6 -0.496 -0.124 -0.067 0.885 0.187 -0.969 -0.81 -0.805 -0.342 0.579 0.003 -0.657 -0.483 -0.341 -0.893 0.502 0.944 0.245 -0.195 0.699 0.047 -0.973 -0.268 0.175 0.684 0.35 0.205 0.167 -0.344 -0.121 -0.318 -0.117 -0.328 0.795 0.206 -0.069 0.572 -0.747 0.634 0.665 -0.606 -0.185 -0.787 -0.118 -0.602 0.377 -0.879 0.529 0.423 -0.419 0.503 -0.836 -0.315 0.712 0.901 -0.973 -0.087 +0 0 0 0 0.833 0.012 0.867 0.733 0.893 0.383 0.567 -0.24 -0.465 -0.578 0.892 0.467 -0.983 0.13 -0.706 -0.884 -0.445 -0.282 0.133 -0.739 0.08 0.679 -0.999 0.17 -0.756 0.984 -0.728 -0.15 -0.965 0.957 -0.848 0.928 0.438 0.257 0.397 0.225 0.295 0.837 -0.47 0.52 0.683 0.741 0.538 0.975 0.443 -0.514 0.728 -0.91 0.181 -0.738 0.673 -0.907 0.824 0.541 0.66 -0.645 -0.423 0.164 -0.866 diff --git a/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-01_dwi.json b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-01_dwi.json new file mode 100644 index 0000000..5cd4faf --- /dev/null +++ b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-01_dwi.json @@ -0,0 +1,48 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.758, + "Manufacturer": "GE", + "InternalPulseSequenceName": "EPI2", + "ManufacturersModelName": "SIGNA Premier", + "BodyPartExamined": "HEAD", + "PatientPosition": "HFS", + "SoftwareVersions": "27\\LX\\MR Software release:RX27.0_R02_1831.a", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_64B1000_5B0", + "ProtocolName": "GENFI2_DWI_64B1000_5B0", + "ScanningSequence": "EP\\SE", + "SequenceVariant": "NONE", + "ScanOptions": "SAT_GEMS\\EPI_GEMS\\ACC_GEMS\\PFF\\FS", + "ImageType": ["ORIGINAL", "PRIMARY", "OTHER"], + "SeriesNumber": 7, + "AcquisitionTime": "15:18:7.000000", + "AcquisitionNumber": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.254732, + "EchoTime": 0.0537, + "RepetitionTime": 6.4, + "FlipAngle": 90, + "PhaseEncodingPolarityGE": "Flipped", + "CoilString": "48HAP", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "AcquisitionMatrixPE": 96, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2.25, + "EffectiveEchoSpacing": 0.000289684, + "TotalReadoutTime": 0.02752, + "PixelBandwidth": 5208.33, + "PhaseEncodingDirection": "j", + "ImageOrientationPatientDICOM": [ + 1, + -0, + 0, + -0, + 0.990516, + -0.137399 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-01_dwi.nii.gz b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-01_dwi.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-02_dwi.bval b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-02_dwi.bval new file mode 100644 index 0000000..fa2b605 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-02_dwi.bval @@ -0,0 +1 @@ +0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 diff --git a/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-02_dwi.bvec b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-02_dwi.bvec new file mode 100644 index 0000000..06205ab --- /dev/null +++ b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-02_dwi.bvec @@ -0,0 +1,3 @@ +0 0 -1 0.422 0.209 -0.8 0.049 0.669 -0.444 0.266 -0.802 0.055 0.357 -0.136 0.296 0.668 0.186 0.742 -0.517 -0.319 0.074 0.817 -0.301 0.628 -0.978 -0.224 0.013 -0.153 -0.598 0.042 0.051 -0.924 0.161 0.238 0.403 0.353 0.841 0.959 -0.858 0.563 -0.933 0.543 -0.672 -0.415 0.363 0.091 -0.586 0.121 0.43 -0.85 -0.329 0.171 0.44 -0.42 -0.607 0.043 -0.26 -0.094 0.682 -0.276 -0.101 0.159 -0.493 +0 0 0 0.907 0.512 -0.6 -0.496 -0.124 -0.067 0.885 0.187 -0.969 -0.81 -0.805 -0.342 0.579 0.003 -0.657 -0.483 -0.341 -0.893 0.502 0.944 0.245 -0.195 0.699 0.047 -0.973 -0.268 0.175 0.684 0.35 0.205 0.167 -0.344 -0.121 -0.318 -0.117 -0.328 0.795 0.206 -0.069 0.572 -0.747 0.634 0.665 -0.606 -0.185 -0.787 -0.118 -0.602 0.377 -0.879 0.529 0.423 -0.419 0.503 -0.836 -0.315 0.712 0.901 -0.973 -0.087 +0 0 0 0 0.833 0.012 0.867 0.733 0.893 0.383 0.567 -0.24 -0.465 -0.578 0.892 0.467 -0.983 0.13 -0.706 -0.884 -0.445 -0.282 0.133 -0.739 0.08 0.679 -0.999 0.17 -0.756 0.984 -0.728 -0.15 -0.965 0.957 -0.848 0.928 0.438 0.257 0.397 0.225 0.295 0.837 -0.47 0.52 0.683 0.741 0.538 0.975 0.443 -0.514 0.728 -0.91 0.181 -0.738 0.673 -0.907 0.824 0.541 0.66 -0.645 -0.423 0.164 -0.866 diff --git a/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-02_dwi.json b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-02_dwi.json new file mode 100644 index 0000000..72772db --- /dev/null +++ b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-02_dwi.json @@ -0,0 +1,48 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 127.758, + "Manufacturer": "GE", + "InternalPulseSequenceName": "EPI2", + "ManufacturersModelName": "SIGNA Premier", + "BodyPartExamined": "HEAD", + "PatientPosition": "HFS", + "SoftwareVersions": "27\\LX\\MR Software release:RX27.0_R02_1831.a", + "MRAcquisitionType": "2D", + "SeriesDescription": "GENFI2_DWI_64B1000_5B0", + "ProtocolName": "GENFI2_DWI_64B1000_5B0", + "ScanningSequence": "EP\\SE", + "SequenceVariant": "NONE", + "ScanOptions": "SAT_GEMS\\EPI_GEMS\\ACC_GEMS\\PFF\\FS", + "ImageType": ["ORIGINAL", "PRIMARY", "OTHER"], + "SeriesNumber": 710, + "AcquisitionTime": "15:18:8.000000", + "AcquisitionNumber": 1, + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "SAR": 0.254732, + "EchoTime": 0.0537, + "RepetitionTime": 6.4, + "FlipAngle": 90, + "PhaseEncodingPolarityGE": "Flipped", + "CoilString": "48HAP", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "AcquisitionMatrixPE": 96, + "ReconMatrixPE": 96, + "ParallelReductionFactorInPlane": 2.25, + "EffectiveEchoSpacing": 0.000289684, + "TotalReadoutTime": 0.02752, + "PixelBandwidth": 5208.33, + "PhaseEncodingDirection": "j", + "ImageOrientationPatientDICOM": [ + 1, + -0, + 0, + -0, + 0.990516, + -0.137399 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20210317" +} diff --git a/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-02_dwi.nii.gz b/tests/data/bids/sub-004/ses-M063/dwi/sub-004_ses-M063_run-02_dwi.nii.gz new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/bids/sub-004/ses-M063/sub-004_ses-M063_scans.tsv b/tests/data/bids/sub-004/ses-M063/sub-004_ses-M063_scans.tsv new file mode 100644 index 0000000..479fa40 --- /dev/null +++ b/tests/data/bids/sub-004/ses-M063/sub-004_ses-M063_scans.tsv @@ -0,0 +1,6 @@ +modality run_num bids_filename manufacturer number_of_parts +T2w run-02 sub-004_ses-M063_run-02_T2w GE MEDICAL SYSTEMS 1 +dwi run-01 sub-004_ses-M063_run-01_dwi GE MEDICAL SYSTEMS 2.0 +T2w run-01 sub-004_ses-M063_run-01_T2w GE MEDICAL SYSTEMS 1 +dwi run-02 sub-004_ses-M063_run-02_dwi GE MEDICAL SYSTEMS 2.0 +T1 run-01 sub-004_ses-M063_run-01_T1w GE MEDICAL SYSTEMS 1 diff --git a/tests/data/bids/sub-004/sub-004_sessions.tsv b/tests/data/bids/sub-004/sub-004_sessions.tsv new file mode 100644 index 0000000..28de822 --- /dev/null +++ b/tests/data/bids/sub-004/sub-004_sessions.tsv @@ -0,0 +1,3 @@ +session_id genfi_version +ses-M000 GENFI1 +ses-M017 GENFI2