diff --git a/example1/resources/map/bidsmap.yaml b/example1/resources/map/bidsmap.yaml index 6a19b29de5b70b369eb44dcdb62cfa0c71446f0f..ab6606a72d2edb17e5c9c33f1d5bef2c74a4552a 100644 --- a/example1/resources/map/bidsmap.yaml +++ b/example1/resources/map/bidsmap.yaml @@ -1,9 +1,4 @@ -Options: - version: 2.3.0 - bidsignore: [] -PlugIns: - path: resources/plugins/bidsify_plugin.py - options: {} +__bids__: 1.2.0 MRI: Nifti_SPM12: __ignore__: @@ -40,7 +35,7 @@ MRI: - echo: ~ json: !!omap - TaskName: <<bids:task>> - - RepetitionTime: <time3:RepetitionTime> + - RepetitionTime: <scale-3:RepetitionTime> - NumberOfVolumesDiscardedByScanner: 0 - NumberOfVolumesDiscardedByUser: 0 - DelayTime: 0 @@ -62,7 +57,7 @@ MRI: - echo: ~ json: !!omap - TaskName: <<bids:task>> - - RepetitionTime: <time3:RepetitionTime> + - RepetitionTime: <scale-3:RepetitionTime> - NumberOfVolumesDiscardedByScanner: 0 - NumberOfVolumesDiscardedByUser: 0 - DelayTime: 0 @@ -83,7 +78,7 @@ MRI: - echo: ~ json: !!omap - TaskName: <<bids:task>> - - RepetitionTime: <time3:RepetitionTime> + - RepetitionTime: <scale-3:RepetitionTime> - NumberOfVolumesDiscardedByScanner: 0 - NumberOfVolumesDiscardedByUser: 0 - DelayTime: 0 @@ -104,7 +99,7 @@ MRI: - echo: ~ json: !!omap - TaskName: <<bids:task>> - - RepetitionTime: <time3:RepetitionTime> + - RepetitionTime: <scale-3:RepetitionTime> - NumberOfVolumesDiscardedByScanner: 0 - NumberOfVolumesDiscardedByUser: 0 - DelayTime: 0 @@ -125,7 +120,7 @@ MRI: - echo: ~ json: !!omap - TaskName: <<bids:task>> - - RepetitionTime: <time3:RepetitionTime> + - RepetitionTime: <scale-3:RepetitionTime> - NumberOfVolumesDiscardedByScanner: 0 - NumberOfVolumesDiscardedByUser: 0 - DelayTime: 0 @@ -144,7 +139,7 @@ MRI: - dir: ~ - run: ~ json: !!omap - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3:EchoTime> - IntendedFor: - "func/<<subject>>_<<session>>_task-nBack_bold.nii" - "func/<<subject>>_<<session>>_task-rest_bold.nii" @@ -162,7 +157,7 @@ MRI: - dir: ~ - run: ~ json: !!omap - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3:EchoTime> - IntendedFor: - "anat/<<subject>>_<<session>>_acq-PDw_echo-*_MPM.nii" - "anat/<<subject>>_<<session>>_acq-MTw_echo-*_MPM.nii" @@ -182,8 +177,8 @@ MRI: - run: ~ json: !!omap - EchoTime: ~ - - EchoTime1: <time6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/0> - - EchoTime2: <time6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/1> + - EchoTime1: <scale-6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/0> + - EchoTime2: <scale-6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/1> - IntendedFor: - "func/<<subject>>_<<session>>_task-nBack_bold.nii" - "func/<<subject>>_<<session>>_task-rest_bold.nii" @@ -202,8 +197,8 @@ MRI: - run: ~ json: !!omap - EchoTime: ~ - - EchoTime1: <time6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/0> - - EchoTime2: <time6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/1> + - EchoTime1: <scale-6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/0> + - EchoTime2: <scale-6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/1> - IntendedFor: - "anat/<<subject>>_<<session>>_acq-PDw_echo-*_MPM.nii" - "anat/<<subject>>_<<session>>_acq-MTw_echo-*_MPM.nii" @@ -219,7 +214,7 @@ MRI: - acq: HeadPDw - mod: ~ json: !!omap - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -233,7 +228,7 @@ MRI: - acq: BodyPDw - mod: ~ json: !!omap - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -246,7 +241,7 @@ MRI: - echo: <EchoNumbers> - fa: <AcquisitionNumber> json: !!omap - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -259,7 +254,7 @@ MRI: - acq: HeadT1w - mod: ~ json: !!omap - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -273,7 +268,7 @@ MRI: json: !!omap - IntendedFor: - "anat/<<subject>>_<<session>>_acq-<<bids:mod>>_echo-*_MPM.nii" - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -287,7 +282,7 @@ MRI: json: !!omap - IntendedFor: - "anat/<<subject>>_<<session>>_acq-<<bids:mod>>_echo-*_MPM.nii" - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -301,7 +296,7 @@ MRI: json: !!omap - IntendedFor: - "anat/<<subject>>_<<session>>_acq-<<bids:mod>>_echo-*_MPM.nii" - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -380,8 +375,8 @@ MRI: - mod: ~ json: !!omap - MTState: "Off" - - EchoTime: <time3:EchoTime> - - RepetitionTime: <time3:RepetitionTime> + - EchoTime: <scale-3:EchoTime> + - RepetitionTime: <scale-3: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 @@ -417,8 +412,8 @@ MRI: - mod: ~ json: !!omap - MTState: "On" - - EchoTime: <time3:EchoTime> - - RepetitionTime: <time3:RepetitionTime> + - EchoTime: <scale-3:EchoTime> + - RepetitionTime: <scale-3: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 @@ -437,8 +432,8 @@ MRI: - mod: ~ json: !!omap - MTState: "Off" - - EchoTime: <time3:EchoTime> - - RepetitionTime: <time3:RepetitionTime> + - EchoTime: <scale-3:EchoTime> + - RepetitionTime: <scale-3: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 @@ -474,6 +469,6 @@ MRI: - mod: ~ json: !!omap - MTState: "On" - - EchoTime: <time3:EchoTime> - - RepetitionTime: <time3:RepetitionTime> + - EchoTime: <scale-3:EchoTime> + - RepetitionTime: <scale-3:RepetitionTime> - FlipAngle: <FlipAngle> diff --git a/example1/resources/map/bidsmap_noPlugin.yaml b/example1/resources/map/bidsmap_noPlugin.yaml index 2ee3709a09fc81daccac7d9e4162346c4e77c274..20c1fbc6d262f1eac6c5fbdd26c2f1fc09465047 100644 --- a/example1/resources/map/bidsmap_noPlugin.yaml +++ b/example1/resources/map/bidsmap_noPlugin.yaml @@ -1,9 +1,4 @@ -Options: - version: 2.3.o - bidsignore: [] -PlugIns: - path: ~ - options: {} +__bids__: 1.2.0 MRI: Nifti_SPM12: __ignore__: @@ -33,7 +28,7 @@ MRI: - echo: ~ json: !!omap - TaskName: <<bids:task>> - - RepetitionTime: <time3:RepetitionTime> + - RepetitionTime: <scale-3:RepetitionTime> - NumberOfVolumesDiscardedByScanner: 0 - NumberOfVolumesDiscardedByUser: 0 - DelayTime: 0 @@ -55,7 +50,7 @@ MRI: - echo: ~ json: !!omap - TaskName: <<bids:task>> - - RepetitionTime: <time3:RepetitionTime> + - RepetitionTime: <scale-3:RepetitionTime> - NumberOfVolumesDiscardedByScanner: 0 - NumberOfVolumesDiscardedByUser: 0 - DelayTime: 0 @@ -76,7 +71,7 @@ MRI: - echo: ~ json: !!omap - TaskName: <<bids:task>> - - RepetitionTime: <time3:RepetitionTime> + - RepetitionTime: <scale-3:RepetitionTime> - NumberOfVolumesDiscardedByScanner: 0 - NumberOfVolumesDiscardedByUser: 0 - DelayTime: 0 @@ -97,7 +92,7 @@ MRI: - echo: ~ json: !!omap - TaskName: <<bids:task>> - - RepetitionTime: <time3:RepetitionTime> + - RepetitionTime: <scale-3:RepetitionTime> - NumberOfVolumesDiscardedByScanner: 0 - NumberOfVolumesDiscardedByUser: 0 - DelayTime: 0 @@ -118,7 +113,7 @@ MRI: - echo: ~ json: !!omap - TaskName: <<bids:task>> - - RepetitionTime: <time3:RepetitionTime> + - RepetitionTime: <scale-3:RepetitionTime> - NumberOfVolumesDiscardedByScanner: 0 - NumberOfVolumesDiscardedByUser: 0 - DelayTime: 0 @@ -137,7 +132,7 @@ MRI: - dir: ~ - run: ~ json: !!omap - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3:EchoTime> - IntendedFor: - "func/<<subject>>_<<session>>_task-nBack_bold.nii" - "func/<<subject>>_<<session>>_task-rest_bold.nii" @@ -155,7 +150,7 @@ MRI: - dir: ~ - run: ~ json: !!omap - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3:EchoTime> - IntendedFor: - "anat/<<subject>>_<<session>>_acq-PDw_echo-*_MPM.nii" - "anat/<<subject>>_<<session>>_acq-MTw_echo-*_MPM.nii" @@ -175,8 +170,8 @@ MRI: - run: ~ json: !!omap - EchoTime: ~ - - EchoTime1: <time6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/0> - - EchoTime2: <time6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/1> + - EchoTime1: <scale-6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/0> + - EchoTime2: <scale-6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/1> - IntendedFor: - "func/<<subject>>_<<session>>_task-nBack_bold.nii" - "func/<<subject>>_<<session>>_task-rest_bold.nii" @@ -195,8 +190,8 @@ MRI: - run: ~ json: !!omap - EchoTime: ~ - - EchoTime1: <time6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/0> - - EchoTime2: <time6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/1> + - EchoTime1: <scale-6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/0> + - EchoTime2: <scale-6:CSASeriesHeaderInfo/MrPhoenixProtocol/alTE/1> - IntendedFor: - "anat/<<subject>>_<<session>>_acq-PDw_echo-*_MPM.nii" - "anat/<<subject>>_<<session>>_acq-MTw_echo-*_MPM.nii" @@ -212,7 +207,7 @@ MRI: - acq: HeadPDw - mod: ~ json: !!omap - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -226,7 +221,7 @@ MRI: - acq: BodyPDw - mod: ~ json: !!omap - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -239,7 +234,7 @@ MRI: - echo: <EchoNumbers> - fa: <AcquisitionNumber> json: !!omap - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -252,7 +247,7 @@ MRI: - acq: HeadT1w - mod: ~ json: !!omap - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -266,7 +261,7 @@ MRI: json: !!omap - IntendedFor: - "anat/<<subject>>_<<session>>_acq-<<bids:mod>>_echo-*_MPM.nii" - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -280,7 +275,7 @@ MRI: json: !!omap - IntendedFor: - "anat/<<subject>>_<<session>>_acq-<<bids:mod>>_echo-*_MPM.nii" - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -294,7 +289,7 @@ MRI: json: !!omap - IntendedFor: - "anat/<<subject>>_<<session>>_acq-<<bids:mod>>_echo-*_MPM.nii" - - EchoTime: <time3:EchoTime> + - EchoTime: <scale-3: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 @@ -373,8 +368,8 @@ MRI: - mod: ~ json: !!omap - MTState: "Off" - - EchoTime: <time3:EchoTime> - - RepetitionTime: <time3:RepetitionTime> + - EchoTime: <scale-3:EchoTime> + - RepetitionTime: <scale-3: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 @@ -409,8 +404,8 @@ MRI: - mod: ~ json: !!omap - MTState: "On" - - EchoTime: <time3:EchoTime> - - RepetitionTime: <time3:RepetitionTime> + - EchoTime: <scale-3:EchoTime> + - RepetitionTime: <scale-3: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 @@ -429,8 +424,8 @@ MRI: - mod: ~ json: !!omap - MTState: "Off" - - EchoTime: <time3:EchoTime> - - RepetitionTime: <time3:RepetitionTime> + - EchoTime: <scale-3:EchoTime> + - RepetitionTime: <scale-3: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 @@ -465,6 +460,6 @@ MRI: - mod: ~ json: !!omap - MTState: "On" - - EchoTime: <time3:EchoTime> - - RepetitionTime: <time3:RepetitionTime> + - EchoTime: <scale-3:EchoTime> + - RepetitionTime: <scale-3:RepetitionTime> - FlipAngle: <FlipAngle>