From 54e382144fb8013eedae87def3512ec74f18bb23 Mon Sep 17 00:00:00 2001 From: Beliy Nikita <beliy.nikita@uliege.be> Date: Mon, 3 Feb 2020 12:28:50 +0100 Subject: [PATCH] added map for ru without plugins --- example1/resources/map/bidsmap_noPlugin.yaml | 503 +++++++++++++++++++ 1 file changed, 503 insertions(+) create mode 100644 example1/resources/map/bidsmap_noPlugin.yaml diff --git a/example1/resources/map/bidsmap_noPlugin.yaml b/example1/resources/map/bidsmap_noPlugin.yaml new file mode 100644 index 0000000..2bf758f --- /dev/null +++ b/example1/resources/map/bidsmap_noPlugin.yaml @@ -0,0 +1,503 @@ +Options: + version: 2.3.1 + bidsignore: [] +PlugIns: + path: ~ + options: {} +MRI: + Nifti_SPM12: + __ignore__: + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-HCL/MRI/001-localizer/s1904-0001-00001-000001-01.nii + checked: true + suffix: '' + attributes: + ProtocolName: 'localizer' + bids: !!omap [] + json: !!omap [] + func: + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-HCL/MRI/002-cmrr_mbep2d_bold_mb2_invertpe/f1904-0002-00001-000001-01.nii + example: func/sub-003_ses-HCL_task-nBack_dir-PA_run-1_bold + checked: true + suffix: bold + attributes: + ProtocolName: cmrr_mbep2d_bold_mb2_invertpe + ImageType: ORIGINAL\\PRIMARY\\M\\MB\\ND\\MOSAIC + SeriesNumber: 2 + bids: !!omap + - dir: PA + - task: nBack + - acq: ~ + - ce: ~ + - rec: ~ + - run: <AcquisitionNumber> + - echo: ~ + json: !!omap + - TaskName: <<bids:task>> + - Instructions: "" + - TaskDescription: "" + - CogAtlasID: "" + - CogPOID: "" + - RepetitionTime: <time3:RepetitionTime> + - NumberOfVolumesDiscardedByScanner: "" + - NumberOfVolumesDiscardedByUser: "" + - DelayTime: 0 + - DelayAfterTrigger: "" + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-HCL/MRI/006-cmrr_mbep2d_bold_mb2_invertpe/f1904-0006-00001-000001-01.nii + example: func/sub-003_ses-HCL_task-rest_dir-PA_run-1_bold + checked: true + suffix: bold + attributes: + ProtocolName: cmrr_mbep2d_bold_mb2_invertpe + ImageType: ORIGINAL\\PRIMARY\\M\\MB\\ND\\MOSAIC + SeriesNumber: 6 + bids: !!omap + - dir: PA + - task: rest + - acq: ~ + - ce: ~ + - rec: ~ + - run: <AcquisitionNumber> + - echo: ~ + json: !!omap + - TaskName: <<bids:task>> + - Instructions: "" + - TaskDescription: "" + - CogAtlasID: "" + - CogPOID: "" + - RepetitionTime: <time3:RepetitionTime> + - NumberOfVolumesDiscardedByScanner: "" + - NumberOfVolumesDiscardedByUser: "" + - DelayTime: 0 + - DelayAfterTrigger: "" + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-HCL/MRI/004-cmrr_mbep2d_bold_mb2_task_fat/f1904-0004-00001-000001-01.nii + example: func/sub-003_ses-HCL_task-nBack_dir-AP_run-1_bold + checked: true + suffix: bold + attributes: + ProtocolName: cmrr_mbep2d_bold_mb2_task_fat + ImageType: ORIGINAL\\PRIMARY\\M\\MB\\ND\\MOSAIC + bids: !!omap + - dir: AP + - task: nBack + - acq: ~ + - ce: ~ + - rec: ~ + - run: <AcquisitionNumber> + - echo: ~ + json: !!omap + - TaskName: <<bids:task>> + - Instructions: "" + - TaskDescription: "" + - CogAtlasID: "" + - CogPOID: "" + - RepetitionTime: <time3:RepetitionTime> + - NumberOfVolumesDiscardedByScanner: "" + - NumberOfVolumesDiscardedByUser: "" + - DelayTime: 0 + - DelayAfterTrigger: "" + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-HCL/MRI/008-cmrr_mbep2d_bold_mb2_rest/f1904-0008-00001-000001-01.nii + example: func/sub-003_ses-HCL_task-rest_dir-AP_run-1_bold + checked: true + suffix: bold + attributes: + ProtocolName: cmrr_mbep2d_bold_mb2_rest + ImageType: ORIGINAL\\PRIMARY\\M\\MB\\ND\\MOSAIC + bids: !!omap + - dir: AP + - task: rest + - acq: ~ + - ce: ~ + - rec: ~ + - run: <AcquisitionNumber> + - echo: ~ + json: !!omap + - TaskName: <<bids:task>> + - Instructions: "" + - TaskDescription: "" + - CogAtlasID: "" + - CogPOID: "" + - RepetitionTime: <time3:RepetitionTime> + - NumberOfVolumesDiscardedByScanner: "" + - NumberOfVolumesDiscardedByUser: "" + - DelayTime: 0 + - DelayAfterTrigger: "" + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-LCL/MRI/004-cmrr_mbep2d_bold_mb2_task_nfat/f1894-0004-00001-000001-01.nii + example: func/sub-003_ses-LCL_task-nBack_dir-AP_run-1_bold + checked: true + suffix: bold + attributes: + ProtocolName: cmrr_mbep2d_bold_mb2_task_nfat + ImageType: ORIGINAL\\PRIMARY\\M\\MB\\ND\\MOSAIC + bids: !!omap + - dir: AP + - task: nBack + - acq: ~ + - ce: ~ + - rec: ~ + - run: <AcquisitionNumber> + - echo: ~ + json: !!omap + - TaskName: <<bids:task>> + - Instructions: "" + - TaskDescription: "" + - CogAtlasID: "" + - CogPOID: "" + - RepetitionTime: <time3:RepetitionTime> + - NumberOfVolumesDiscardedByScanner: "" + - NumberOfVolumesDiscardedByUser: "" + - DelayTime: 0 + - DelayAfterTrigger: "" + fmap: + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-HCL/MRI/010-gre_field_mapping/s1904-0010-00001-000001-01.nii + example: fmap/sub-003_ses-HCL_magnitude1 + checked: true + suffix: magnitude<EchoNumbers> + attributes: + ProtocolName: 'gre_field_mapping' + ImageType: 'ORIGINAL\\PRIMARY\\M\\ND' + SeriesNumber: 10 + bids: !!omap + - acq: ~ + - ce: ~ + - dir: ~ + - run: ~ + json: !!omap + - EchoTime: <time3:EchoTime> + - IntendedFor: + - "func/<<subject>>_<<session>>_task-nBack_bold.nii" + - "func/<<subject>>_<<session>>_task-rest_bold.nii" + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/015-gre_field_mapping/s1905-0015-00001-000001-01.nii + example: fmap/sub-003_ses-STROOP_magnitude1 + checked: true + suffix: magnitude<EchoNumbers> + attributes: + ProtocolName: 'gre_field_mapping' + ImageType: 'ORIGINAL\\PRIMARY\\M\\ND' + SeriesNumber: 15 + bids: !!omap + - acq: ~ + - ce: ~ + - dir: ~ + - run: ~ + json: !!omap + - EchoTime: <time3:EchoTime> + - IntendedFor: + - "anat/<<subject>>_<<session>>_acq-PDw_echo-*_MPM.nii" + - "anat/<<subject>>_<<session>>_acq-MTw_echo-*_MPM.nii" + - "anat/<<subject>>_<<session>>_acq-T1w_echo-*_MPM.nii" + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-HCL/MRI/011-gre_field_mapping/s1904-0011-00001-000001-02.nii + example: fmap/sub-003_ses-HCL_phasediff + checked: true + suffix: phasediff + attributes: + ProtocolName: 'gre_field_mapping' + ImageType: 'ORIGINAL\\PRIMARY\\P\\ND' + SeriesNumber: 11 + bids: !!omap + - acq: ~ + - ce: ~ + - dir: ~ + - run: ~ + json: !!omap + - EchoTime: ~ + - EchoTime1: <time6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/0> + - EchoTime2: <time6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/1> + - IntendedFor: + - "func/<<subject>>_<<session>>_task-nBack_bold.nii" + - "func/<<subject>>_<<session>>_task-rest_bold.nii" + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/016-gre_field_mapping/s1905-0016-00001-000001-02.nii + example: fmap/sub-003_ses-STROOP_phasediff + checked: true + suffix: phasediff + attributes: + ProtocolName: 'gre_field_mapping' + ImageType: 'ORIGINAL\\PRIMARY\\P\\ND' + SeriesNumber: 16 + bids: !!omap + - acq: ~ + - ce: ~ + - dir: ~ + - run: ~ + json: !!omap + - EchoTime: ~ + - EchoTime1: <time6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/0> + - EchoTime2: <time6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/1> + - IntendedFor: + - "anat/<<subject>>_<<session>>_acq-PDw_echo-*_MPM.nii" + - "anat/<<subject>>_<<session>>_acq-MTw_echo-*_MPM.nii" + - "anat/<<subject>>_<<session>>_acq-T1w_echo-*_MPM.nii" + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/002-al_mtflash3d_sensArray/s1905-0002-00001-000032-01.nii + example: fmap/sub-003_ses-STROOP_acq-HeadPDw_B1minus + checked: true + suffix: B1minus + attributes: + ProtocolName: 'al_mtflash3d_sensArray' + SeriesNumber: 2 + bids: !!omap + - acq: HeadPDw + - mod: ~ + json: !!omap + - EchoTime: <time3:EchoTime> + - IntendedFor: + - "anat/<<subject>>_<<session>>_acq-<<bids:mod>>_echo-*_MPM.nii" + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/003-al_mtflash3d_sensBody/s1905-0003-00001-000032-01.nii + example: fmap/sub-003_ses-STROOP_acq-BodyPDw_B1minus + checked: true + suffix: B1minus + attributes: + ProtocolName: 'al_mtflash3d_sensBody' + SeriesNumber: 3 + bids: !!omap + - acq: BodyPDw + - mod: ~ + json: !!omap + - EchoTime: <time3:EchoTime> + - IntendedFor: + - "anat/<<subject>>_<<session>>_acq-<<bids:mod>>_echo-*_MPM.nii" + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/014-al_B1mapping/s1905-0014-00001-000001-01.nii + example: fmap/sub-003_ses-STROOP_echo-1_fa-1_B1plus + checked: true + suffix: B1plus + attributes: + ProtocolName: 'al_B1mapping' + bids: !!omap + - echo: <EchoNumbers> + - fa: <AcquisitionNumber> + json: !!omap + - EchoTime: <time3:EchoTime> + - B1mapNominalFAValues: <B1mapNominalFAValues> + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/006-al_mtflash3d_sensArray/s1905-0006-00001-000032-01.nii + example: fmap/sub-003_ses-STROOP_acq-HeadT1w_B1minus + checked: true + suffix: B1minus + attributes: + ProtocolName: 'al_mtflash3d_sensArray' + SeriesNumber: 6 + bids: !!omap + - acq: HeadT1w + - mod: ~ + json: !!omap + - EchoTime: <time3:EchoTime> + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/007-al_mtflash3d_sensBody/s1905-0007-00001-000032-01.nii + example: fmap/sub-003_ses-STROOP_acq-BodyT1w_B1minus + checked: true + suffix: B1minus + attributes: + ProtocolName: 'al_mtflash3d_sensBody' + SeriesNumber: 7 + bids: !!omap + - acq: BodyT1w + - mod: ~ + json: !!omap + - IntendedFor: + - "anat/<<subject>>_<<session>>_acq-<<bids:mod>>_echo-*_MPM.nii" + - EchoTime: <time3:EchoTime> + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/010-al_mtflash3d_sensArray/s1905-0010-00001-000032-01.nii + example: fmap/sub-003_ses-STROOP_acq-HeadMTw_B1minus + checked: true + suffix: B1minus + attributes: + ProtocolName: 'al_mtflash3d_sensArray' + SeriesNumber: 10 + bids: !!omap + - acq: HeadMTw + - mod: ~ + json: !!omap + - IntendedFor: + - "anat/<<subject>>_<<session>>_acq-<<bids:mod>>_echo-*_MPM.nii" + - EchoTime: <time3:EchoTime> + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/011-al_mtflash3d_sensBody/s1905-0011-00001-000032-01.nii + example: fmap/sub-003_ses-STROOP_acq-BodyMTw_B1minus + checked: true + suffix: B1minus + attributes: + ProtocolName: 'al_mtflash3d_sensBody' + SeriesNumber: 11 + bids: !!omap + - acq: BodyMTw + - mod: ~ + json: !!omap + - IntendedFor: + - "anat/<<subject>>_<<session>>_acq-<<bids:mod>>_echo-*_MPM.nii" + - EchoTime: <time3:EchoTime> + dwi: + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-HCL/MRI/012-cmrr_mbep2d_diff_NODDI_invertpe/s1904-0012-00001-000001-01.nii + example: dwi/sub-003_ses-HCL_acq-RF_dir-PA_run-1_dwi + checked: true + suffix: dwi + attributes: + ProtocolName: cmrr_mbep2d_diff_NODDI_invertpe + bids: !!omap + - dir: PA + - acq: RF + - run: <AcquisitionNumber> + json: !!omap [] + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-HCL/MRI/013-cmrr_mbep2d_diff_NODDI/f1904-0013-00001-000001-01.nii + example: dwi/sub-003_ses-HCL_acq-RF_dir-AP_run-1_dwi + checked: true + suffix: dwi + attributes: + ProtocolName: cmrr_mbep2d_diff_NODDI + bids: !!omap + - dir: AP + - acq: RF + - run: <AcquisitionNumber> + json: !!omap [] + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-HCL/MRI/014-cmrr_mbep2d_diff_NODDI_noise/s1904-0014-00001-000001-01.nii + example: dwi/sub-003_ses-HCL_acq-noRF_dir-AP_run-1_dwi + checked: true + suffix: dwi + attributes: + ProtocolName: cmrr_mbep2d_diff_NODDI_noise + bids: !!omap + - dir: AP + - acq: noRF + - run: <AcquisitionNumber> + json: !!omap [] + anat: + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-LCL/MRI/012-t1_mpr_sag_p2_iso/s1894-0012-00001-000224-01.nii + example: anat/sub-003_ses-LCL_T1w + checked: true + suffix: T1w + attributes: + ProtocolName: t1_mpr_sag_p2_iso + bids: !!omap + - acq: ~ + - ce: ~ + - rec: ~ + - run: ~ + - mod: ~ + json: !!omap + - ContrastBolusIngredient: ~ + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-LCL/MRI/013-t2_spc_da-fl_sag_p2_iso/s1894-0013-00001-000192-01.nii + example: anat/sub-003_ses-LCL_FLAIR + checked: true + suffix: FLAIR + attributes: + ProtocolName: 't2_spc_da-fl_sag_p2_iso' + bids: !!omap + - acq: ~ + - ce: ~ + - rec: ~ + - run: ~ + - mod: ~ + json: !!omap + - ContrastBolusIngredient: ~ + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/004-al_mtflash3d_PDw/s1905-0004-00001-000176-01.nii + example: anat/sub-003_ses-STROOP_acq-PDw_part-mag_echo-1_MPM + checked: true + suffix: MPM + attributes: + ProtocolName: 'al_mtflash3d_PDw' + ImageType: 'ORIGINAL\\PRIMARY\\M\\ND' + bids: !!omap + - acq: PDw + - ce: ~ + - rec: ~ + - part: mag + - run: ~ + - echo: <EchoNumbers> + - mod: ~ + json: !!omap + - MTState: "Off" + - ContrastBolusIngredient: ~ + - EchoTime: <time3:EchoTime> + - RepetitionTime: <time3:RepetitionTime> + - FlipAngle: <FlipAngle> + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/008-al_mtflash3d_T1w/s1905-0008-00001-000176-01.nii + example: anat/sub-003_ses-STROOP_acq-T1w_part-mag_echo-1_MPM + checked: true + suffix: MPM + attributes: + ProtocolName: al_mtflash3d_T1w + ImageType: 'ORIGINAL\\PRIMARY\\M\\ND' + bids: !!omap + - acq: T1w + - part: mag + - ce: ~ + - rec: ~ + - run: ~ + - mod: ~ + - echo: <EchoNumbers> + json: !!omap + - ContrastBolusIngredient: ~ + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/012-al_mtflash3d_MTw/s1905-0012-00001-000176-01.nii + example: anat/sub-003_ses-STROOP_acq-MTw_part-mag_echo-1_MPM + checked: true + suffix: MPM + attributes: + ProtocolName: 'al_mtflash3d_MTw' + ImageType: 'ORIGINAL\\PRIMARY\\M\\ND' + bids: !!omap + - acq: MTw + - ce: ~ + - rec: ~ + - part: mag + - run: ~ + - echo: <EchoNumbers> + - mod: ~ + json: !!omap + - MTState: "On" + - ContrastBolusIngredient: ~ + - EchoTime: <time3:EchoTime> + - RepetitionTime: <time3:RepetitionTime> + - FlipAngle: <FlipAngle> + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/005-al_mtflash3d_PDw/s1905-0005-00001-000176-01.nii + example: anat/sub-003_ses-STROOP_acq-PDw_part-phase_echo-1_MPM + checked: true + suffix: MPM + attributes: + ProtocolName: 'al_mtflash3d_PDw' + ImageType: 'ORIGINAL\\PRIMARY\\P\\ND' + bids: !!omap + - acq: PDw + - ce: ~ + - rec: ~ + - part: phase + - run: ~ + - echo: <EchoNumbers> + - mod: ~ + json: !!omap + - MTState: "Off" + - ContrastBolusIngredient: ~ + - EchoTime: <time3:EchoTime> + - RepetitionTime: <time3:RepetitionTime> + - FlipAngle: <FlipAngle> + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/009-al_mtflash3d_T1w/s1905-0009-00001-000176-01.nii + example: anat/sub-003_ses-STROOP_acq-T1w_part-phase_echo-1_T1w + checked: true + suffix: MPM + attributes: + ProtocolName: al_mtflash3d_T1w + ImageType: 'ORIGINAL\\PRIMARY\\P\\ND' + bids: !!omap + - acq: T1w + - part: phase + - ce: ~ + - rec: ~ + - run: ~ + - mod: ~ + - echo: <EchoNumbers> + json: !!omap + - ContrastBolusIngredient: ~ + - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/013-al_mtflash3d_MTw/s1905-0013-00001-000176-01.nii + example: anat/sub-003_ses-STROOP_acq-MTw_part-phase_echo-1_MPM + checked: true + suffix: MPM + attributes: + ProtocolName: 'al_mtflash3d_MTw' + ImageType: 'ORIGINAL\\PRIMARY\\P\\ND' + bids: !!omap + - acq: MTw + - ce: ~ + - rec: ~ + - part: phase + - run: ~ + - echo: <EchoNumbers> + - mod: ~ + json: !!omap + - MTState: "On" + - ContrastBolusIngredient: ~ + - EchoTime: <time3:EchoTime> + - RepetitionTime: <time3:RepetitionTime> + - FlipAngle: <FlipAngle> -- GitLab