Initial import

.gitignore

+*.pyc
+.idea
+*.IMA
+*.swp
+dist
+build
+bidscoin.egg-info
+.coverage
+.vscode
+venv
+.eggs
+htmlcov
+__pycache__
+.tox
+tests/testdata/*.log
+tests/testdata/bidsmap_output.yaml
+test/

README.md

+This folder contains toy datasets inspired from real ones but with removed 
+data and keeping meta-information to minimum. The demographic informations
+and subjects id are randomised.
+
+Each example folder contains 3 subfolders:
+ - source, containing the original toy dataset
+ - renamed, containing sorted dataset
+ - bids, containing bidsified dataset
+ - resources, containing all nessesairy plugins and files to run the example
+
+## Example 1
+Example 1 is based on unpublished study on effet of fatigue on memory performance.
+
+

example1/bids/.gitignore

+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

example1/renamed/.gitignore

+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

example1/resources/FCsepNBack.json

+{
+  "onset":{
+    "LongName":"Onset (in seconds) of the event",
+    "Description":"Onset (in seconds) of the event measured from the beginning of the acquisition of the first volume in the corresponding task imaging data file.",
+    "Units":"s"
+  },
+  "duration":{
+    "LongName":"Time that stimulus was presented",
+    "Units":"s"
+  },
+  "response_time":{
+    "LongName":"Time taked to respond to stimulus",
+    "Units":"s"
+  },
+  "trial_type":{
+    "LongName":"Condition presented to subject",
+    "Levels":{
+      "Test_1Back":"",
+      "Test_2Back":"",
+      "Test_3Back":""
+    }
+  },
+  "block":{
+    "LongName":"Id of block for trial"
+  },
+  "value":{
+    "LongName":"Recieved responce",
+    "Levels":{
+      "c":"correct",
+      "n":"non correct"
+    }
+  },
+  "exp_value":{
+    "LongName":"Expected responce",
+    "Levels":{
+      "c":"correct",
+      "n":"non correct"
+    }
+  }
+}
\ No newline at end of file

example1/resources/VAS.json

+{
+  "trial_type":{
+    "LongName":"Asked question",
+    "Description":"State evaluation question",
+    "Levels":{
+      "Motivation":"Estimation of motivation",
+      "Happiness":"Estimation of happiness",
+      "Fatigue":"Estimation of fatigue",
+      "Openness":"Estimation of openness",
+      "Stress":"Estimation of stress",
+      "Anxiety":"Estimation of anxiety",
+      "Effort":"Estimation of effort"
+    }
+  },
+  "stim_file":{
+    "LongName":"Image presented during question"
+  },
+  "value":{
+    "LongName":"Recieved estimation value",
+    "Description":"Recieved estimation value in scale from 0 to 100"
+  }
+}
\ No newline at end of file

example1/resources/map/bidsmap.yaml

+Options:
+  version: 2.3.1
+  bidsignore: []
+PlugIns:
+  path: test/resources/plugin/bidsify_plugin.py
+  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 []
+      - provenance: /home/beliy/Works/bidscoin/test/renamed/sub-003/ses-STROOP/MRI/002-al_mtflash3d_sensArray/s1905-0002-00001-000032-01.nii
+        checked: true
+        suffix: ''
+        attributes:
+          SeriesDescription: 'invalid'
+        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
+          SeriesDescription: 'nBack'
+        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
+          SeriesDescription: 'rest'
+        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'
+          SeriesDescription: 'HCL/LCL'
+        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'
+          SeriesDescription: 'STROOP'
+        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'
+          SeriesDescription: 'HCL/LCL'
+        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'
+          SeriesDescription: 'STROOP'
+        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'
+          SeriesDescription: 'PDw'
+        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'
+          SeriesDescription: 'PDw'
+        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'
+          SeriesDescription: 'T1w'
+        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'
+          SeriesDescription: 'T1w'
+        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'
+          SeriesDescription: 'MTw'
+        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'
+          SeriesDescription: 'MTw'
+        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>

example1/resources/participants.json

+{
+  "participant_id":{
+    "LongName":"Participant Id",
+    "Description":"label identifying a particular subject"
+  },
+  "age":{
+    "LongName":"Age",
+    "Description":"Age of a subject",
+    "Units":"year"
+  },
+  "sex":{
+    "LongName":"Sex",
+    "Description":"Sex of a subject",
+    "Levels":{
+      "F":"Female",
+      "M":"Male"
+    }
+  },
+  "education":{
+    "LongName":"Education level",
+    "Description":"Education level"
+  },
+  "group":{
+    "LongName":"group",
+    "Description":"Group subject belongs",
+    "Levels":{
+      "patient":"patient",
+      "control":"control"
+    }
+  },
+  "handiness":{
+    "LongName":"Handiness of subject",
+    "Levels":{
+      "r":"right-handed",
+      "l":"left-handed"
+    }
+  },
+  "paired":{
+    "LongName":"Paired Id",
+    "Description":"Subject Id paired with this subject"
+  },
+  "ses_1":{
+    "LongName":"First session",
+    "Description":"Id of the first session taken by subject",
+    "Levels":{
+      "ses-LCL":"Low charge level",
+      "ses-HCL":"High charge level",
+      "ses-STROOP":"Multiparametric scan"
+    }
+  },
+  "ses_2":{
+    "LongName":"Second session",
+    "Description":"Id of the second session taken by subject",
+    "Levels":{
+      "ses-LCL":"Low charge level",
+      "ses-HCL":"High charge level",
+      "ses-STROOP":"Multiparametric scan"
+    }
+  },
+  "ses_3":{
+    "LongName":"Third session",
+    "Description":"Id of the second session taken by subject",
+    "Levels":{
+      "ses-LCL":"Low charge level",
+      "ses-HCL":"High charge level",
+      "ses-STROOP":"Multiparametric scan"
+    }
+  }
+}
\ No newline at end of file

example1/resources/plugins/bidsify_plugin.py

+import os
+import shutil
+import logging
+import pandas
+
+import Modules
+
+from definitions import Series, checkSeries
+
+logger = logging.getLogger(__name__)
+
+# global variables
+rawfolder = ""
+bidsfolder = ""
+dry_run = False
+
+participants_table = None
+rec_path = ""
+countSeries = {}
+
+
+def InitEP(source: str, destination: str, dry: bool) -> int:
+    global rawfolder
+    global bidsfolder
+    global dry_run
+
+    rawfolder = source
+    bidsfolder = destination
+    dry_run = dry
+
+    participants = os.path.join(rawfolder, "participants.tsv")
+    if not os.path.isfile(participants):
+        e = "participants.tsv not found in {}".format(rawfolder)
+        logger.critical(e)
+        raise FileNotFoundError("participants.tsv not found")
+
+    global participants_table
+    participants_table = pandas.read_csv(participants, sep='\t',
+                                         header=0,
+                                         index_col="participant_id",
+                                         na_values="n/a")
+
+    participants_table = participants_table.groupby("participant_id")\
+        .ffill().drop_duplicates()
+    duplicates = participants_table.index.duplicated(keep=False)
+    if duplicates.any():
+        logger.error("One or several subjects have conflicting values."
+                     "See {} for details"
+                     .format(participants))
+        raise KeyError("Conflicting values in subject descriptions")
+    Modules.baseModule.sub_BIDSfields.LoadDefinitions(os.path.join(rawfolder, 
+                                                      "participants.json"))
+
+def SessionEP(scan):
+    global series
+    global sid
+    sub = scan["subject"]
+    ses = scan["session"]
+    path = os.path.join(rawfolder,
+                        sub, ses,
+                        "MRI")
+    series = sorted(os.listdir(path))
+    series = [s.split("-",1)[1] for s in series]
+    sid = -1
+    checkSeries(path, sub, ses, False)
+    # copytng behevioral data
+    aux_input = os.path.join(rawfolder, sub, ses, "aux")
+    if ses in ("ses-LCL", "ses-HCL"):
+        if not os.path.isdir(aux_input):
+            logger.error("Session {}/{} do not contain aux folder"
+                         .format(sub, ses))
+            raise FileNotFoundError("folder {} not found"
+                                    .format(aux_input))
+        beh = os.path.join(bidsfolder, sub, ses, "beh")
+        if not dry_run:
+            os.makedirs(beh, exist_ok=True)
+        for old, new in (("FCsepNBack.tsv", "task-rest_events.tsv"),
+                         ("FCsepNBack.json", "task-rest_events.json"),
+                         ("VAS.tsv", "task-rest_beh.tsv"),
+                         ("VAS.json", "task-rest_beh.json")):
+            source = "{}/{}".format(aux_input, old)
+            dest = "{}/{}_{}_{}".format(beh, sub, ses, new)
+            if not os.path.isfile(source):
+                if dry_run:
+                    logger.error("{}/{}: File {} not found"
+                                 .format(sub, ses, source))
+                else:
+                    logger.critical("{}/{}: File {} not found"
+                                    .format(sub, ses, source))
+                    raise FileNotFoundError(source)
+            if os.path.isfile(dest):
+                logger.warning("{}/{}: File {} already exists"
+                               .format(sub, ses, dest))
+            if not dry_run:
+                shutil.copy2(source, dest)
+
+
+series = list()
+sid = -1
+Intended = ""
+
+def SequenceEP(recording):
+    global series
+    global sid
+    global Intended
+    Intended = ""
+    sub = recording.subId()
+    part = participants_table.loc[sub]
+    for f in participants_table.columns:
+        recording.sub_BIDSvalues[f] = part[f]
+    sid += 1
+    recid = series[sid] 
+    if recid != recording.recId():
+        logger.warning("{}: Id mismatch folder {}"
+                       .format(recording.recIdentity(False),
+                                recid))
+    if recid == "cmrr_mbep2d_bold_mb2_invertpe":
+        mod = series[sid + 1]
+        if mod.endswith("cmrr_mbep2d_bold_mb2_task_fat"):
+            Intended = "nBack"
+        elif mod.endswith("cmrr_mbep2d_bold_mb2_task_nfat"):
+            Intended = "nBack"
+        elif mod.endswith("cmrr_mbep2d_bold_mb2_rest"):
+            Intended = "rest"
+        else:
+            Intended = "invalid"
+            logger.warning("{}: Unknown session {}"
+                           .format(recording.recIdentity(),
+                                   mod))
+    elif recid == "gre_field_mapping":
+        if recording.sesId() in ("ses-HCL", "ses-LCL"):
+            Intended = "HCL/LCL"
+        elif recording.sesId() == "ses-STROOP":
+            Intended = "STROOP"
+        else:
+            logger.warning("{}: Unknown session {}"
+                           .format(recording.recIdentity(),
+                                   recording.sesId()))
+            Intended = "invalid"
+    elif recid == "al_mtflash3d_sensArray":
+        det = series[sid + 2]
+        if det.endswith("al_mtflash3d_PDw"):
+            Intended = "PDw"
+        elif det.endswith("al_mtflash3d_T1w"):
+            Intended = "T1w"
+            recording.setAttribute("Intended", "T1w")
+        elif det.endswith("al_mtflash3d_MTw"):
+            Intended = "MTw"
+        else:
+            logger.warning("{}: Unable determine modality"
+                           .format(recording.recIdentity()))
+            Intended = "invalid"
+    elif recid == "al_mtflash3d_sensBody":
+        det = series[sid + 1]
+        if det.endswith("al_mtflash3d_PDw"):
+            Intended = "PDw"
+        elif det.endswith("al_mtflash3d_T1w"):
+            Intended = "T1w"
+        elif det.endswith("al_mtflash3d_MTw"):
+            Intended = "MTw"
+        else:
+            logger.warning("{}: Unable determine modality"
+                           .format(recording.recIdentity()))
+            Intended = "invalid"
+
+
+def RecordingEP(recording):
+    if Intended != "":
+        recording.setAttribute("SeriesDescription", Intended)

example1/resources/plugins/definitions.py

+import logging
+import os
+
+logger = logging.getLogger(__name__)
+
+Series = {
+        "ses-LCL": ('localizer',
+                    'cmrr_mbep2d_bold_mb2_invertpe', 
+                    'cmrr_mbep2d_bold_mb2_task_nfat', 
+                    'cmrr_mbep2d_bold_mb2_invertpe', 
+                    'cmrr_mbep2d_bold_mb2_rest',
+                    'gre_field_mapping',
+                    'gre_field_mapping',
+                    't1_mpr_sag_p2_iso',
+                    't2_spc_da-fl_sag_p2_iso'
+                    ),
+        "ses-HCL": ('localizer',
+                    'cmrr_mbep2d_bold_mb2_invertpe',
+                    'cmrr_mbep2d_bold_mb2_task_fat',
+                    'cmrr_mbep2d_bold_mb2_invertpe',
+                    'cmrr_mbep2d_bold_mb2_rest',
+                    'gre_field_mapping',
+                    'gre_field_mapping',
+                    'cmrr_mbep2d_diff_NODDI_invertpe',
+                    'cmrr_mbep2d_diff_NODDI',
+                    'cmrr_mbep2d_diff_NODDI_noise'
+                    ),
+        "ses-STROOP": ('localizer',
+                       'al_mtflash3d_sensArray',
+                       'al_mtflash3d_sensBody',
+                       'al_mtflash3d_PDw',
+                       'al_mtflash3d_PDw',
+                       'al_mtflash3d_sensArray',
+                       'al_mtflash3d_sensBody',
+                       'al_mtflash3d_T1w',
+                       'al_mtflash3d_T1w',
+                       'al_mtflash3d_sensArray',
+                       'al_mtflash3d_sensBody',
+                       'al_mtflash3d_MTw',
+                       'al_mtflash3d_MTw',
+                       'al_B1mapping',
+                       'gre_field_mapping',
+                       'gre_field_mapping'
+                       )
+        }
+
+
+countSeries = {}
+for ses in Series:
+    countSeries[ses] = dict.fromkeys(Series[ses], 0)
+    for ser in Series[ses]:
+        countSeries[ses][ser] += 1
+
+
+def checkSeries(path: str,
+                subject: str, session: str,
+                critical: bool) -> None:
+    """
+    Retrieve list of series from path and checks 
+    its compatibility with defined list
+
+    Parameters:
+    -----------
+    path: str
+        Path to folder containing series folder
+    subject: str
+        Subject id
+    session: str
+        Name of session to check
+    critical: bool
+        If True, mismatches will creeate exceptions 
+        and critical level log entries
+    """
+    if session not in Series:
+        msg = "{}/{}: Invalid session".format(subject, session)
+        reportError(msg, critical, KeyError)
+        return
+    passed = True
+    series = sorted(os.listdir(path))
+    series = [s.split("-",1)[1] for s in series]
+    for ind, s in enumerate(series):
+        if s not in Series[session]:
+            msg = "{}/{}: Invalid serie {}".format(subject, session, s)
+            logger.error(msg)
+            passed = False
+            continue
+        if s == "cmrr_mbep2d_bold_mb2_invertpe":
+            if ind >= len(series) or\
+                    series[ind + 1] not in ("cmrr_mbep2d_bold_mb2_task_nfat",
+                                            "cmrr_mbep2d_bold_mb2_task_fat",
+                                            "cmrr_mbep2d_bold_mb2_rest"):
+                msg = "{}/{}: {:03}-{} isn't followed by task recording"\
+                    .format(subject, session, ind, s)
+                logger.error(msg)
+                passed = False
+        elif s == "al_mtflash3d_sensArray":
+            if ind >= len(series) - 1 or\
+                    series[ind + 2] not in ("al_mtflash3d_PDw",
+                                            "al_mtflash3d_MTw",
+                                            "al_mtflash3d_T1w"):
+                msg = "{}/{}: {:03}-{} isn't followed by weighted recording"\
+                        .format(subject, session, ind, s)
+                logger.error(msg)
+                passed = False
+        elif s == "al_mtflash3d_sensBody":
+            if ind >= len(series) or\
+                    series[ind + 1] not in ("al_mtflash3d_PDw",
+                                            "al_mtflash3d_MTw",
+                                            "al_mtflash3d_T1w"):
+                msg = "{}/{}: {:03}-{} isn't followed by weighted recording"\
+                        .format(subject, session, ind, s)
+                logger.error(msg)
+                passed = False
+
+    for ser, count in countSeries[session].items():
+        count_loc = series.count(ser)
+        if count != count_loc:
+            msg = "{}/{}: Expected {} occurences of {}, got {}"\
+                    .format(subject, session, count, ser, count_loc)
+            logger.error(msg)
+            passed = False
+
+    if not passed:
+        msg = "{}/{}: One or several series errors detected"\
+                .format(subject, session)
+        reportError(msg, critical, ValueError)
+    return passed
+
+
+def reportError(msg: str, critical: bool, error: type=ValueError) -> None:
+    """
+    reports error. 
+    If critical, an exception of type error will raise
+
+    Parametres:
+    -----------
+    msg: str
+        message to report
+    critical: bool
+        determines level of error
+    error: exception
+        type of exception to raise in case of critical
+    """
+    if critical:
+        logger.critical(msg)
+        raise exception(msg)
+    else:
+        logger.error(msg)

example1/resources/plugins/rename_plugin.py

+import os
+import pandas
+import glob
+import logging
+import shutil
+
+from tools import tools 
+from bidsMeta import BIDSfieldLibrary
+
+from definitions import Series, checkSeries
+
+logger = logging.getLogger(__name__)
+
+# global variables
+rawfolder = ""
+bidsfolder = ""
+dry_run = False
+
+
+resources = os.path.join(os.path.dirname(__file__), "..")
+
+df_subjects = None
+scans_map = {}
+
+# scale to convert ms in log-files to seconds
+time_scale = 1e-3
+
+# list of subjects exel-file columns 
+excel_col_list = {'Patient' : 'pat',
+                  'S_A_E' : "pat_sae",
+                  1: "pat_1", 2: "pat_2", 3: "pat_3",
+                  'Control' : "cnt",
+                  'S_A_E.1': "cnt_sae",
+                  '1.1': "cnt_1", '2.1': "cnt_2", '3.1': "cnt_3",
+                  }
+
+sub_columns = BIDSfieldLibrary()
+
+def InitEP(source: str, destination: str,
+           dry: bool,
+           subjects: str="") -> int:
+    global rawfolder
+    global bidsfolder
+    global dry_run
+    global subject_file
+
+    rawfolder = source
+    bidsfolder = destination
+    dry_run = dry
+    if subjects:
+        subject_file = subjects
+    else:
+        subject_file = os.path.join(resources, "Appariement.xlsx")
+    logger.info(subject_file)
+
+    if not os.path.isfile(subject_file):
+        raise FileNotFoundError("Subject file '{}' not found"
+                                .format(subject_file))
+
+    # generating model participants.tsv
+    model_participants = os.path.join(resources, "participants.json")
+    sub_columns.LoadDefinitions(model_participants)
+
+    # creating df for subjects
+    global df_subjects
+    df_subjects = pandas.read_excel(subject_file,
+                                    sheet_name=0, header=0,
+                                    usecols=[0,1,2,3,4,5,6,7,8,9,10])
+    df_subjects.rename(index=str, columns=excel_col_list,inplace=True)
+    df_subjects = df_subjects[df_subjects['pat'].notnull()
+                              | df_subjects['cnt'].notnull()]
+
+
+def SubjectEP(session):
+    sub_id = int(session["subject"])
+    index = df_subjects.loc[df_subjects["pat"] == sub_id].index 
+    status = 0
+    prefix = "pat"
+    if len(index) == 0:
+        # Subject not in patient list, looking in control
+        index = df_subjects.loc[df_subjects["cnt"] == sub_id].index
+        if len(index) == 0:
+            raise KeyError("Subject {} not found in table"
+                           .format(sub_id))
+        status = 1
+        prefix = "cnt"
+    index = index[0]
+
+    # retrieving demographics
+    # <sex>_<age>_<education>
+    line = df_subjects.loc[index, prefix + "_sae"].split("_")
+    sex = line[0]
+    age = int(line[1])
+    education = int(line[2])
+    values = sub_columns.GetTemplate()
+    values["participant_id"] = "sub-" + session["subject"]
+    values["sex"] = sex
+    values["age"] = age
+    values["education"] = education
+
+    # looking for pairing
+    if status == 0:
+        values["group"] = "patient"
+        values["paired"] = "sub-{:03}".format(int(df_subjects
+                                                  .loc[index, "cnt"]))
+    else:
+        values["group"] = "control"
+        values["paired"] = "sub-{:03}".format(int(df_subjects
+                                                  .loc[index, "pat"]))
+
+    # looking for order of sessions
+    global scans_map
+    scans_map = {}
+    scans_order = sorted([os.path.basename(s) for s in
+                          tools.lsdirs(os.path.join(rawfolder,
+                                                    session["subject"]),
+                                       "s*")
+                          ])
+    for ind, s in enumerate(("_1", "_2", "_3")):
+        v = "ses-" + str(df_subjects.loc[index, prefix + s]).strip()
+        ses = "ses" + s
+        if v == "ses-nan":
+            values[ses] = ""
+            logger.warning("Subject {}({}): missing {} value"
+                           .format(values["participant_id"],
+                                   values["group"],
+                                   ses)
+                           )
+        elif v not in Series:
+            logger.critical("Subject {}({}): Invalid {}: {}"
+                            .format(values["participant_id"],
+                                    values["group"],
+                                    ses,
+                                    values[ses])
+                            )
+            raise KeyError("Invalid {}: {}"
+                           .format(ses, v))
+        else:
+            values[ses] = v
+            scans_map[scans_order[ind]] = values[ses]
+
+    # checking if all scans are identifyable
+    for scan in scans_order:
+        if scan not in scans_map:
+            logger.error("Subject {}({}): Can't identify session {}"
+                         .format(values["participant_id"],
+                                 values["group"],
+                                 scan))
+            scans_map[scan] = scan
+
+    # creating tsv file
+    tsv_file = os.path.join(bidsfolder, "participants.tsv")
+    if not os.path.isfile(tsv_file):
+        with open(tsv_file, 'w') as f:
+            f.write(sub_columns.GetHeader())
+            f.write("\n")
+    with open(os.path.join(bidsfolder, "participants.tsv"), "a") as f:
+        f.write(sub_columns.GetLine(values))
+        f.write("\n")
+    model_participants = os.path.join(bidsfolder, "participants.json")
+    if not os.path.isfile(model_participants):
+        sub_columns.DumpDefinitions(model_participants)
+
+    session["subject"] = "sub-" + session["subject"]
+    return 0
+
+
+def SessionEP(session):
+    # retrieving correct session name
+    session["session"] = scans_map[session["session"]]
+    return 0
+
+
+def SessionEndEP(session):
+    res = checkSeries(os.path.join(session["out_path"], "MRI"),
+                      session["subject"], session["session"],
+                      False)
+
+    # parcing log files
+    if session["session"] == "ses-STROOP":
+        return 0
+
+    logs = os.path.join(session["in_path"], "inp")
+    aux_d = os.path.join(session["out_path"], "aux")
+    if not os.path.isdir(logs):
+        raise NotADirectoryError(logs)
+
+    os.makedirs(aux_d, exist_ok=True)
+    for file in ("FCsepNBack.tsv", "VAS.tsv"):
+        file = os.path.join(logs, file)
+        if not os.path.isfile(file):
+            raise FileNotFoundError(file)
+        shutil.copy2(file, aux_d)
+
+    for file in ("FCsepNBack.json", "VAS.json"):
+        file = os.path.join(resources, file)
+        if not os.path.isfile(file):
+            raise FileNotFoundError(file)
+        shutil.copy2(file, aux_d)
+    
+    return 0

example1/source/001/s01512/inp/FCsepNBack.tsv

+onset	duration	response_time	trial_type	block	value	exp_value
+16.942	1.70	n/a	Test_1Back	1	n/a	n/a
+19.142	1.70	0.859	Test_1Back	1	c	c
+21.342	1.70	0.872	Test_1Back	1	n	n
+23.542	1.70	0.919	Test_1Back	1	c	c
+25.742	1.70	0.988	Test_1Back	1	n	n
+27.942	1.70	0.910	Test_1Back	1	n	n
+30.142	1.70	0.956	Test_1Back	1	n	n
+32.342	1.70	0.777	Test_1Back	1	n	n
+34.542	1.70	0.890	Test_1Back	1	n	n
+36.742	1.70	1.001	Test_1Back	1	n	n
+38.942	1.70	0.894	Test_1Back	1	c	c
+41.142	1.70	0.860	Test_1Back	1	n	c
+43.342	1.70	1.008	Test_1Back	1	n	n
+45.542	1.70	0.628	Test_1Back	1	n	n
+47.742	1.70	0.991	Test_1Back	1	c	c
+49.942	1.70	0.907	Test_1Back	1	c	c
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+74.342	1.70	n/a	Test_2Back	2	n/a	n/a
+76.542	1.70	0.970	Test_2Back	2	c	c
+78.742	1.70	1.039	Test_2Back	2	n	n
+80.942	1.70	0.874	Test_2Back	2	n	n
+83.142	1.70	1.188	Test_2Back	2	c	c
+85.342	1.70	1.135	Test_2Back	2	n	n
+87.542	1.70	0.868	Test_2Back	2	c	c
+89.742	1.70	0.911	Test_2Back	2	n	n
+91.942	1.70	1.126	Test_2Back	2	n	n
+94.142	1.70	0.970	Test_2Back	2	c	c
+96.342	1.70	0.959	Test_2Back	2	c	c
+98.542	1.70	0.906	Test_2Back	2	c	c
+100.742	1.70	0.893	Test_2Back	2	n	n
+102.942	1.70	1.143	Test_2Back	2	c	c
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+129.542	1.70	n/a	Test_3Back	3	n/a	n/a
+131.742	1.70	n/a	Test_3Back	3	n/a	n/a
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+138.342	1.70	1.198	Test_3Back	3	n	n
+140.542	1.70	0.991	Test_3Back	3	c	c
+142.742	1.70	1.019	Test_3Back	3	n	n
+144.942	1.70	1.099	Test_3Back	3	c	c
+147.142	1.70	0.975	Test_3Back	3	c	c
+149.342	1.70	1.113	Test_3Back	3	n	n
+151.542	1.70	1.031	Test_3Back	3	c	c
+153.742	1.70	1.033	Test_3Back	3	n	n
+155.942	1.70	1.143	Test_3Back	3	n	n
+158.142	1.70	1.197	Test_3Back	3	c	c
+160.342	1.70	1.039	Test_3Back	3	c	c
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+184.742	1.70	0.827	Test_1Back	4	n	n
+186.942	1.70	0.847	Test_1Back	4	c	c
+189.142	1.70	1.075	Test_1Back	4	n	n
+191.342	1.70	0.999	Test_1Back	4	c	c
+193.542	1.70	0.928	Test_1Back	4	n	n
+195.742	1.70	0.914	Test_1Back	4	n	n
+197.942	1.70	0.953	Test_1Back	4	n	n
+200.142	1.70	0.889	Test_1Back	4	n	n
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+204.542	1.70	1.042	Test_1Back	4	c	c
+206.742	1.70	0.905	Test_1Back	4	n	n
+208.942	1.70	1.013	Test_1Back	4	n	n
+211.142	1.70	0.936	Test_1Back	4	n	n
+213.342	1.70	1.073	Test_1Back	4	n	n
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+239.942	1.70	n/a	Test_2Back	5	n/a	n/a
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+244.342	1.70	1.052	Test_2Back	5	c	c
+246.542	1.70	0.805	Test_2Back	5	c	c
+248.742	1.70	0.882	Test_2Back	5	c	c
+250.942	1.70	1.061	Test_2Back	5	n	n
+253.142	1.70	0.726	Test_2Back	5	c	c
+255.342	1.70	1.145	Test_2Back	5	c	c
+257.542	1.70	1.057	Test_2Back	5	n	n
+259.742	1.70	0.946	Test_2Back	5	c	c
+261.942	1.70	0.955	Test_2Back	5	c	c
+264.142	1.70	1.030	Test_2Back	5	n	n
+266.342	1.70	0.967	Test_2Back	5	n	n
+268.542	1.70	1.021	Test_2Back	5	n	n
+270.742	1.70	0.915	Test_2Back	5	n	c
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+295.142	1.70	n/a	Test_3Back	6	n/a	n/a
+297.342	1.70	n/a	Test_3Back	6	n/a	n/a
+299.542	1.70	1.125	Test_3Back	6	c	c
+301.742	1.70	1.020	Test_3Back	6	n	n
+303.942	1.70	1.231	Test_3Back	6	c	c
+306.142	1.70	1.089	Test_3Back	6	n	n
+308.342	1.70	1.131	Test_3Back	6	c	c
+310.542	1.70	0.927	Test_3Back	6	n	n
+312.742	1.70	1.268	Test_3Back	6	n	n
+314.942	1.70	1.223	Test_3Back	6	n	n
+317.142	1.70	1.260	Test_3Back	6	n	n
+319.342	1.70	0.933	Test_3Back	6	c	c
+321.542	1.70	1.072	Test_3Back	6	c	c
+323.742	1.70	1.025	Test_3Back	6	n	c
+325.942	1.70	1.190	Test_3Back	6	c	c
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+350.342	1.70	0.814	Test_1Back	7	n	n
+352.542	1.70	0.952	Test_1Back	7	n	n
+354.742	1.70	0.827	Test_1Back	7	n	n
+356.942	1.70	0.798	Test_1Back	7	n	n
+359.142	1.70	0.929	Test_1Back	7	c	c
+361.342	1.70	0.743	Test_1Back	7	c	c
+363.542	1.70	1.113	Test_1Back	7	n	n
+365.742	1.70	0.930	Test_1Back	7	n	n
+367.942	1.70	0.896	Test_1Back	7	c	c
+370.142	1.70	0.799	Test_1Back	7	n	n
+372.342	1.70	0.914	Test_1Back	7	c	c
+374.542	1.70	0.955	Test_1Back	7	n	n
+376.742	1.70	0.984	Test_1Back	7	n	n
+378.942	1.70	0.857	Test_1Back	7	n	n
+381.142	1.70	0.949	Test_1Back	7	n	n
+403.342	1.70	n/a	Test_2Back	8	n/a	n/a
+405.542	1.70	n/a	Test_2Back	8	n/a	n/a
+407.742	1.70	1.086	Test_2Back	8	c	c
+409.942	1.70	0.978	Test_2Back	8	c	c
+412.142	1.70	1.021	Test_2Back	8	c	c
+414.342	1.70	1.152	Test_2Back	8	c	c
+416.542	1.70	1.125	Test_2Back	8	n	c
+418.742	1.70	0.962	Test_2Back	8	c	c
+420.942	1.70	1.023	Test_2Back	8	n	n
+423.142	1.70	1.010	Test_2Back	8	c	n
+425.342	1.70	0.947	Test_2Back	8	c	c
+427.542	1.70	1.075	Test_2Back	8	c	c
+429.742	1.70	1.178	Test_2Back	8	c	c
+431.942	1.70	1.162	Test_2Back	8	c	c
+434.142	1.70	1.286	Test_2Back	8	c	c
+436.342	1.70	1.093	Test_2Back	8	c	c
+458.542	1.70	n/a	Test_3Back	9	n/a	n/a
+460.742	1.70	n/a	Test_3Back	9	n/a	n/a
+462.942	1.70	n/a	Test_3Back	9	n/a	n/a
+465.142	1.70	1.031	Test_3Back	9	c	c
+467.342	1.70	1.277	Test_3Back	9	c	c
+469.542	1.70	0.888	Test_3Back	9	n	n
+471.742	1.70	1.185	Test_3Back	9	c	c
+473.942	1.70	1.172	Test_3Back	9	n	n
+476.142	1.70	1.312	Test_3Back	9	c	c
+478.342	1.70	1.016	Test_3Back	9	c	c
+480.542	1.70	0.923	Test_3Back	9	n	n
+482.742	1.70	1.099	Test_3Back	9	c	c
+484.942	1.70	1.119	Test_3Back	9	n	n
+487.142	1.70	0.974	Test_3Back	9	c	c
+489.342	1.70	1.210	Test_3Back	9	n	n
+491.542	1.70	1.125	Test_3Back	9	n	n
+513.742	1.70	n/a	Test_1Back	10	n/a	n/a
+515.942	1.70	0.744	Test_1Back	10	c	c
+518.142	1.70	0.863	Test_1Back	10	c	c
+520.342	1.70	0.974	Test_1Back	10	n	n
+522.542	1.70	0.902	Test_1Back	10	n	n
+524.742	1.70	0.956	Test_1Back	10	c	c
+526.942	1.70	0.938	Test_1Back	10	n	n
+529.142	1.70	0.804	Test_1Back	10	c	c
+531.342	1.70	0.906	Test_1Back	10	n	n
+533.542	1.70	1.049	Test_1Back	10	c	c
+535.742	1.70	0.973	Test_1Back	10	c	c
+537.942	1.70	1.012	Test_1Back	10	n	n
+540.142	1.70	0.937	Test_1Back	10	n	n
+542.342	1.70	0.969	Test_1Back	10	n	n
+544.542	1.70	0.907	Test_1Back	10	c	c
+546.742	1.70	0.863	Test_1Back	10	n	n
+568.942	1.70	n/a	Test_2Back	11	n/a	n/a
+571.142	1.70	n/a	Test_2Back	11	n/a	n/a
+573.342	1.70	0.944	Test_2Back	11	c	c
+575.542	1.70	0.985	Test_2Back	11	c	c
+577.742	1.70	1.111	Test_2Back	11	n	n
+579.942	1.70	1.091	Test_2Back	11	n	n
+582.142	1.70	0.998	Test_2Back	11	n	n
+584.342	1.70	1.115	Test_2Back	11	c	c
+586.542	1.70	1.070	Test_2Back	11	n	n
+588.742	1.70	1.041	Test_2Back	11	n	n
+590.942	1.70	0.927	Test_2Back	11	n	n
+593.142	1.70	1.078	Test_2Back	11	n	c
+595.342	1.70	1.125	Test_2Back	11	n	n
+597.542	1.70	0.982	Test_2Back	11	c	c
+599.742	1.70	0.972	Test_2Back	11	n	n
+601.942	1.70	0.933	Test_2Back	11	c	n
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+626.342	1.70	n/a	Test_3Back	12	n/a	n/a
+628.542	1.70	n/a	Test_3Back	12	n/a	n/a
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+632.942	1.70	1.061	Test_3Back	12	n	n
+635.142	1.70	1.127	Test_3Back	12	n	n
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+639.542	1.70	1.105	Test_3Back	12	c	c
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+643.942	1.70	1.128	Test_3Back	12	n	n
+646.142	1.70	0.985	Test_3Back	12	c	c
+648.342	1.70	1.095	Test_3Back	12	c	c
+650.542	1.70	1.186	Test_3Back	12	n	n
+652.742	1.70	1.088	Test_3Back	12	n	n
+654.942	1.70	1.263	Test_3Back	12	n	n
+657.142	1.70	1.186	Test_3Back	12	n	n
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+683.742	1.70	0.713	Test_1Back	13	c	c
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+688.142	1.70	0.890	Test_1Back	13	n	n
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+694.742	1.70	0.764	Test_1Back	13	n	n
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+705.742	1.70	0.798	Test_1Back	13	n	n
+707.942	1.70	1.096	Test_1Back	13	n	n
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+712.342	1.70	0.928	Test_1Back	13	n	n
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+736.742	1.70	n/a	Test_2Back	14	n/a	n/a
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+741.142	1.70	1.036	Test_2Back	14	n	n
+743.342	1.70	1.129	Test_2Back	14	c	c
+745.542	1.70	1.056	Test_2Back	14	c	c
+747.742	1.70	0.943	Test_2Back	14	c	c
+749.942	1.70	1.035	Test_2Back	14	c	c
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+754.342	1.70	0.962	Test_2Back	14	c	c
+756.542	1.70	1.107	Test_2Back	14	n	n
+758.742	1.70	1.039	Test_2Back	14	c	c
+760.942	1.70	0.931	Test_2Back	14	c	c
+763.142	1.70	0.926	Test_2Back	14	c	c
+765.342	1.70	0.909	Test_2Back	14	n	n
+767.542	1.70	0.988	Test_2Back	14	n	n
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+791.942	1.70	n/a	Test_3Back	15	n/a	n/a
+794.142	1.70	n/a	Test_3Back	15	n/a	n/a
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+798.542	1.70	1.101	Test_3Back	15	n	n
+800.742	1.70	1.188	Test_3Back	15	c	c
+802.942	1.70	1.180	Test_3Back	15	n	n
+805.142	1.70	1.093	Test_3Back	15	c	c
+807.342	1.70	1.113	Test_3Back	15	n	n
+809.542	1.70	1.295	Test_3Back	15	c	c
+811.742	1.70	1.195	Test_3Back	15	c	c
+813.942	1.70	1.029	Test_3Back	15	n	n
+816.142	1.70	1.081	Test_3Back	15	c	c
+818.342	1.70	1.144	Test_3Back	15	n	n
+820.542	1.70	1.204	Test_3Back	15	c	c
+822.742	1.70	1.152	Test_3Back	15	n	n
+844.942	1.70	n/a	Test_1Back	16	n/a	n/a
+847.142	1.70	0.780	Test_1Back	16	n	n
+849.342	1.70	0.740	Test_1Back	16	c	n
+851.542	1.70	0.729	Test_1Back	16	n	n
+853.742	1.70	0.862	Test_1Back	16	n	n
+855.942	1.70	0.954	Test_1Back	16	n	n
+858.142	1.70	0.562	Test_1Back	16	n	n
+860.342	1.70	0.903	Test_1Back	16	n	n
+862.542	1.70	0.799	Test_1Back	16	c	c
+864.742	1.70	0.867	Test_1Back	16	n	n
+866.942	1.70	0.978	Test_1Back	16	c	c
+869.142	1.70	0.915	Test_1Back	16	c	n
+871.342	1.70	0.905	Test_1Back	16	c	c
+873.542	1.70	0.903	Test_1Back	16	n	n
+875.742	1.70	0.923	Test_1Back	16	c	c
+877.942	1.70	0.872	Test_1Back	16	c	c
+900.142	1.70	n/a	Test_2Back	17	n/a	n/a
+902.342	1.70	n/a	Test_2Back	17	n/a	n/a
+904.542	1.70	0.870	Test_2Back	17	c	c
+906.742	1.70	0.926	Test_2Back	17	n	n
+908.942	1.70	1.065	Test_2Back	17	n	n
+911.142	1.70	0.997	Test_2Back	17	c	c
+913.342	1.70	0.925	Test_2Back	17	n	n
+915.542	1.70	1.087	Test_2Back	17	c	c
+917.742	1.70	0.898	Test_2Back	17	n	n
+919.942	1.70	1.036	Test_2Back	17	n	n
+922.142	1.70	0.957	Test_2Back	17	c	c
+924.342	1.70	0.913	Test_2Back	17	c	c
+926.542	1.70	1.050	Test_2Back	17	n	n
+928.742	1.70	1.018	Test_2Back	17	n	c
+930.942	1.70	0.832	Test_2Back	17	c	c
+933.142	1.70	0.916	Test_2Back	17	c	c
+955.342	1.70	n/a	Test_3Back	18	n/a	n/a
+957.542	1.70	n/a	Test_3Back	18	n/a	n/a
+959.742	1.70	n/a	Test_3Back	18	n/a	n/a
+961.942	1.70	0.990	Test_3Back	18	c	c
+964.142	1.70	1.284	Test_3Back	18	c	c
+966.342	1.70	1.168	Test_3Back	18	c	c
+968.542	1.70	1.129	Test_3Back	18	n	n
+970.742	1.70	1.108	Test_3Back	18	c	c
+972.942	1.70	1.100	Test_3Back	18	c	c
+975.142	1.70	1.108	Test_3Back	18	n	n
+977.342	1.70	1.172	Test_3Back	18	c	c
+979.542	1.70	0.851	Test_3Back	18	c	c
+981.742	1.70	0.948	Test_3Back	18	n	n
+983.942	1.70	1.087	Test_3Back	18	c	c
+986.142	1.70	1.149	Test_3Back	18	n	n
+988.342	1.70	1.078	Test_3Back	18	c	c

example1/source/001/s01512/inp/VAS.tsv

+trial_type	stim_file	value
+Motivation	Vas/images/VAS.0.bmp	46.56
+Happiness	Vas/images/VAS.1.bmp	68.80
+Fatigue	Vas/images/VAS.2.bmp	48.03
+Openness	Vas/images/VAS.3.bmp	32.02
+Stress	Vas/images/VAS.4.bmp	59.46
+Anxiety	Vas/images/VAS.5.bmp	60.13
+Effort	Vas/images/VAS.6.bmp	48.91

example1/source/001/s01512/nii/f1512-0002-00001-000001-01.nii

+f1512-0002-00001-000001-01.nii
\ No newline at end of file

example1/source/001/s01512/nii/f1512-0002-00002-000002-01.nii

+f1512-0002-00002-000002-01.nii
\ No newline at end of file

example1/source/001/s01512/nii/f1512-0002-00003-000003-01.nii

+f1512-0002-00003-000003-01.nii
\ No newline at end of file