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 # vpinhibition
-Repository for the code of the Inhibition Experiment
+Repository for the code of the Inhibition Experiment: *"A human cortical adaptive mutual inhibition circuit underlying competition for perceptual decision and repetition suppression reversal"*.
 
-**Authors:** Teresa Sousa, Alexandre Sayal, Ricardo Martins, João Duarte, Gabriel Costa
-
-Visual Perception group at the Coimbra Institute for Biomedical Imaging and Translational Research [(CIBIT)](https://www.uc.pt/en/uid/cibit), University of Coimbra, Portugal.
+**Authors:**
+Visual Perception group at the Coimbra Institute for Biomedical Imaging and Translational Research [(CIBIT)](https://www.uc.pt/en/uid/cibit), University of Coimbra, Portugal:
+- [Teresa Sousa](https://github.com/SousaT)
+- [Alexandre Sayal](https://github.com/alexsayal)
+- [Ricardo Martins](https://github.com/ricardomar)
+- [João Duarte](https://github.com/joaovduarte)
+- [Gabriel Costa](https://github.com/gcosta18)
+- [Miguel Castelo-Branco](https://github.com/mcastelobranco)
 
 ---
 
 ## Index
-1. **scripts-01-protocolcreator** 
+1. **scripts-01-protocolcreator** - scripts for creating the protocols in BrainVoyager format.
 2. **scripts-02-stimulus** - stimulus scripts.
 3. **scripts-03-keypress** - scripts for analysing keypress data.
 4. **scripts-04-eyetracker** - scripts for analysing eyetracker data.
 5. **scripts-05-pipelineA-spm** - scripts for analysing fMRI data with SPM (pipeline A).
-6. **scripts-06-pipelineB-bids** - scripts for organizing fMRI data to BIDS (pipeline B).
-7. **scripts-07-pipelineB-fmriprep** - scripts for running fmriPrep (pipeline B).
-8. **scripts-08-pipelineB-spm** - scripts for analyzing fMRI data with SPM after fmriPrep preprocessing (pipeline B).
+6. **scripts-06-pipelineA-analysis** - scripts for extracting time courses and estimating ERAs (pipeline A).
+7. **scripts-07-pipelineB-bids** - scripts for organizing fMRI data to BIDS (pipeline B).
+8. **scripts-08-pipelineB-fmriprep** - scripts for running fmriPrep (pipeline B).
+9. **scripts-09-pipelineB-spm** - scripts for analyzing fMRI data with SPM after fmriPrep preprocessing (pipeline B), extracting time courses and estimating ERAs.
 
 ---
 ## Requirements

diff --git a/...eA-analysis/Configs_VP_INHIBITION_SPM.mat → ...eA-analysis/Configs_VP_INHIBITION_SPM.mat b/...eA-analysis/Configs_VP_INHIBITION_SPM.mat → ...eA-analysis/Configs_VP_INHIBITION_SPM.mat
diff --git a/scripts-05-pipelineA-analysis/ExpC_ERA_SPM.m → scripts-06-pipelineA-analysis/ExpC_ERA_SPM.m b/scripts-05-pipelineA-analysis/ExpC_ERA_SPM.m → scripts-06-pipelineA-analysis/ExpC_ERA_SPM.m
diff --git a/...5-pipelineA-analysis/ExpC_ERA_SPM_Group.m → ...6-pipelineA-analysis/ExpC_ERA_SPM_Group.m b/...5-pipelineA-analysis/ExpC_ERA_SPM_Group.m → ...6-pipelineA-analysis/ExpC_ERA_SPM_Group.m
diff --git a/scripts-05-pipelineA-analysis/FiguresPaper.m → scripts-06-pipelineA-analysis/FiguresPaper.m b/scripts-05-pipelineA-analysis/FiguresPaper.m → scripts-06-pipelineA-analysis/FiguresPaper.m
diff --git a/scripts-05-pipelineA-analysis/README.md → scripts-06-pipelineA-analysis/README.md b/scripts-05-pipelineA-analysis/README.md → scripts-06-pipelineA-analysis/README.md
diff --git a/...pts-05-pipelineA-analysis/TC_Extraction.m → ...pts-06-pipelineA-analysis/TC_Extraction.m b/...pts-05-pipelineA-analysis/TC_Extraction.m → ...pts-06-pipelineA-analysis/TC_Extraction.m
diff --git a/scripts-05-pipelineA-analysis/readProtocol.m → scripts-06-pipelineA-analysis/readProtocol.m b/scripts-05-pipelineA-analysis/readProtocol.m → scripts-06-pipelineA-analysis/readProtocol.m
diff --git a/...ineB-bids/ConvertPRTtoTSVplusCopyToBIDS.m → ...ineB-bids/ConvertPRTtoTSVplusCopyToBIDS.m b/...ineB-bids/ConvertPRTtoTSVplusCopyToBIDS.m → ...ineB-bids/ConvertPRTtoTSVplusCopyToBIDS.m
diff --git a/...pts-06-pipelineB-bids/CopyConvertPhysio.m → ...pts-07-pipelineB-bids/CopyConvertPhysio.m b/...pts-06-pipelineB-bids/CopyConvertPhysio.m → ...pts-07-pipelineB-bids/CopyConvertPhysio.m
diff --git a/scripts-06-pipelineB-bids/README.md → scripts-07-pipelineB-bids/README.md b/scripts-06-pipelineB-bids/README.md → scripts-07-pipelineB-bids/README.md
diff --git a/scripts-06-pipelineB-bids/readProtocol.m → scripts-07-pipelineB-bids/readProtocol.m b/scripts-06-pipelineB-bids/readProtocol.m → scripts-07-pipelineB-bids/readProtocol.m
diff --git a/...elineB-bids/temp-tsv/task-run1_events.tsv → ...elineB-bids/temp-tsv/task-run1_events.tsv b/...elineB-bids/temp-tsv/task-run1_events.tsv → ...elineB-bids/temp-tsv/task-run1_events.tsv
diff --git a/...elineB-bids/temp-tsv/task-run2_events.tsv → ...elineB-bids/temp-tsv/task-run2_events.tsv b/...elineB-bids/temp-tsv/task-run2_events.tsv → ...elineB-bids/temp-tsv/task-run2_events.tsv
diff --git a/...elineB-bids/temp-tsv/task-run3_events.tsv → ...elineB-bids/temp-tsv/task-run3_events.tsv b/...elineB-bids/temp-tsv/task-run3_events.tsv → ...elineB-bids/temp-tsv/task-run3_events.tsv
diff --git a/...elineB-bids/temp-tsv/task-run4_events.tsv → ...elineB-bids/temp-tsv/task-run4_events.tsv b/...elineB-bids/temp-tsv/task-run4_events.tsv → ...elineB-bids/temp-tsv/task-run4_events.tsv
diff --git a/...elineB-bids/temp-tsv/task-run5_events.tsv → ...elineB-bids/temp-tsv/task-run5_events.tsv b/...elineB-bids/temp-tsv/task-run5_events.tsv → ...elineB-bids/temp-tsv/task-run5_events.tsv
diff --git a/...elineB-bids/temp-tsv/task-run6_events.tsv → ...elineB-bids/temp-tsv/task-run6_events.tsv b/...elineB-bids/temp-tsv/task-run6_events.tsv → ...elineB-bids/temp-tsv/task-run6_events.tsv
diff --git a/scripts-07-pipelineB-fmriprep/README.md → scripts-08-pipelineB-fmriprep/README.md b/scripts-07-pipelineB-fmriprep/README.md → scripts-08-pipelineB-fmriprep/README.md
diff --git a/scripts-07-pipelineB-fmriprep/Scripts.txt → scripts-08-pipelineB-fmriprep/Scripts.txt b/scripts-07-pipelineB-fmriprep/Scripts.txt → scripts-08-pipelineB-fmriprep/Scripts.txt
diff --git a/...s/vpinhibition-fmriprep-sub01-logfile.txt → ...s/vpinhibition-fmriprep-sub01-logfile.txt b/...s/vpinhibition-fmriprep-sub01-logfile.txt → ...s/vpinhibition-fmriprep-sub01-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub02-logfile.txt → ...s/vpinhibition-fmriprep-sub02-logfile.txt b/...s/vpinhibition-fmriprep-sub02-logfile.txt → ...s/vpinhibition-fmriprep-sub02-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub03-logfile.txt → ...s/vpinhibition-fmriprep-sub03-logfile.txt b/...s/vpinhibition-fmriprep-sub03-logfile.txt → ...s/vpinhibition-fmriprep-sub03-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub04-logfile.txt → ...s/vpinhibition-fmriprep-sub04-logfile.txt b/...s/vpinhibition-fmriprep-sub04-logfile.txt → ...s/vpinhibition-fmriprep-sub04-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub05-logfile.txt → ...s/vpinhibition-fmriprep-sub05-logfile.txt b/...s/vpinhibition-fmriprep-sub05-logfile.txt → ...s/vpinhibition-fmriprep-sub05-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub06-logfile.txt → ...s/vpinhibition-fmriprep-sub06-logfile.txt b/...s/vpinhibition-fmriprep-sub06-logfile.txt → ...s/vpinhibition-fmriprep-sub06-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub07-logfile.txt → ...s/vpinhibition-fmriprep-sub07-logfile.txt b/...s/vpinhibition-fmriprep-sub07-logfile.txt → ...s/vpinhibition-fmriprep-sub07-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub08-logfile.txt → ...s/vpinhibition-fmriprep-sub08-logfile.txt b/...s/vpinhibition-fmriprep-sub08-logfile.txt → ...s/vpinhibition-fmriprep-sub08-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub09-logfile.txt → ...s/vpinhibition-fmriprep-sub09-logfile.txt b/...s/vpinhibition-fmriprep-sub09-logfile.txt → ...s/vpinhibition-fmriprep-sub09-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub10-logfile.txt → ...s/vpinhibition-fmriprep-sub10-logfile.txt b/...s/vpinhibition-fmriprep-sub10-logfile.txt → ...s/vpinhibition-fmriprep-sub10-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub11-logfile.txt → ...s/vpinhibition-fmriprep-sub11-logfile.txt b/...s/vpinhibition-fmriprep-sub11-logfile.txt → ...s/vpinhibition-fmriprep-sub11-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub12-logfile.txt → ...s/vpinhibition-fmriprep-sub12-logfile.txt b/...s/vpinhibition-fmriprep-sub12-logfile.txt → ...s/vpinhibition-fmriprep-sub12-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub13-logfile.txt → ...s/vpinhibition-fmriprep-sub13-logfile.txt b/...s/vpinhibition-fmriprep-sub13-logfile.txt → ...s/vpinhibition-fmriprep-sub13-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub14-logfile.txt → ...s/vpinhibition-fmriprep-sub14-logfile.txt b/...s/vpinhibition-fmriprep-sub14-logfile.txt → ...s/vpinhibition-fmriprep-sub14-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub15-logfile.txt → ...s/vpinhibition-fmriprep-sub15-logfile.txt b/...s/vpinhibition-fmriprep-sub15-logfile.txt → ...s/vpinhibition-fmriprep-sub15-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub16-logfile.txt → ...s/vpinhibition-fmriprep-sub16-logfile.txt b/...s/vpinhibition-fmriprep-sub16-logfile.txt → ...s/vpinhibition-fmriprep-sub16-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub17-logfile.txt → ...s/vpinhibition-fmriprep-sub17-logfile.txt b/...s/vpinhibition-fmriprep-sub17-logfile.txt → ...s/vpinhibition-fmriprep-sub17-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub18-logfile.txt → ...s/vpinhibition-fmriprep-sub18-logfile.txt b/...s/vpinhibition-fmriprep-sub18-logfile.txt → ...s/vpinhibition-fmriprep-sub18-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub19-logfile.txt → ...s/vpinhibition-fmriprep-sub19-logfile.txt b/...s/vpinhibition-fmriprep-sub19-logfile.txt → ...s/vpinhibition-fmriprep-sub19-logfile.txt
diff --git a/...s/vpinhibition-fmriprep-sub20-logfile.txt → ...s/vpinhibition-fmriprep-sub20-logfile.txt b/...s/vpinhibition-fmriprep-sub20-logfile.txt → ...s/vpinhibition-fmriprep-sub20-logfile.txt
diff --git a/...pipelineB-spm/BackupManuallyDefinedROIs.m → ...pipelineB-spm/BackupManuallyDefinedROIs.m b/...pipelineB-spm/BackupManuallyDefinedROIs.m → ...pipelineB-spm/BackupManuallyDefinedROIs.m
diff --git a/scripts-08-pipelineB-spm/ClearSPMMats.m → scripts-09-pipelineB-spm/ClearSPMMats.m b/scripts-08-pipelineB-spm/ClearSPMMats.m → scripts-09-pipelineB-spm/ClearSPMMats.m
diff --git a/scripts-08-pipelineB-spm/ERA-data.mat → scripts-09-pipelineB-spm/ERA-data.mat b/scripts-08-pipelineB-spm/ERA-data.mat → scripts-09-pipelineB-spm/ERA-data.mat
diff --git a/...08-pipelineB-spm/Output_20230712-1938.mat → ...09-pipelineB-spm/Output_20230712-1938.mat b/...08-pipelineB-spm/Output_20230712-1938.mat → ...09-pipelineB-spm/Output_20230712-1938.mat
diff --git a/scripts-08-pipelineB-spm/PeakCoordinates.mat → scripts-09-pipelineB-spm/PeakCoordinates.mat b/scripts-08-pipelineB-spm/PeakCoordinates.mat → scripts-09-pipelineB-spm/PeakCoordinates.mat
diff --git a/scripts-08-pipelineB-spm/README.md → scripts-09-pipelineB-spm/README.md b/scripts-08-pipelineB-spm/README.md → scripts-09-pipelineB-spm/README.md
diff --git a/scripts-08-pipelineB-spm/Step01_MainSPM.m → scripts-09-pipelineB-spm/Step01_MainSPM.m b/scripts-08-pipelineB-spm/Step01_MainSPM.m → scripts-09-pipelineB-spm/Step01_MainSPM.m
diff --git a/...8-pipelineB-spm/Step02_ExtractTCfromROI.m → ...9-pipelineB-spm/Step02_ExtractTCfromROI.m b/...8-pipelineB-spm/Step02_ExtractTCfromROI.m → ...9-pipelineB-spm/Step02_ExtractTCfromROI.m
diff --git a/...s-08-pipelineB-spm/Step03_CalculateERAs.m → ...s-09-pipelineB-spm/Step03_CalculateERAs.m b/...s-08-pipelineB-spm/Step03_CalculateERAs.m → ...s-09-pipelineB-spm/Step03_CalculateERAs.m
diff --git a/...-08-pipelineB-spm/Step04_ExtractTvalues.m → ...-09-pipelineB-spm/Step04_ExtractTvalues.m b/...-08-pipelineB-spm/Step04_ExtractTvalues.m → ...-09-pipelineB-spm/Step04_ExtractTvalues.m
diff --git a/...elineB-spm/TimeSeries_PeakCoordinates.mat → ...elineB-spm/TimeSeries_PeakCoordinates.mat b/...elineB-spm/TimeSeries_PeakCoordinates.mat → ...elineB-spm/TimeSeries_PeakCoordinates.mat
diff --git a/scripts-08-pipelineB-spm/computePhysIO.m → scripts-09-pipelineB-spm/computePhysIO.m b/scripts-08-pipelineB-spm/computePhysIO.m → scripts-09-pipelineB-spm/computePhysIO.m
diff --git a/...s-08-pipelineB-spm/createConfoundMatrix.m → ...s-09-pipelineB-spm/createConfoundMatrix.m b/...s-08-pipelineB-spm/createConfoundMatrix.m → ...s-09-pipelineB-spm/createConfoundMatrix.m
diff --git a/scripts-08-pipelineB-spm/executeMultiRun.m → scripts-09-pipelineB-spm/executeMultiRun.m b/scripts-08-pipelineB-spm/executeMultiRun.m → scripts-09-pipelineB-spm/executeMultiRun.m
diff --git a/scripts-08-pipelineB-spm/executeSPMjob.m → scripts-09-pipelineB-spm/executeSPMjob.m b/scripts-08-pipelineB-spm/executeSPMjob.m → scripts-09-pipelineB-spm/executeSPMjob.m
diff --git a/scripts-08-pipelineB-spm/extractROIdata.m → scripts-09-pipelineB-spm/extractROIdata.m b/scripts-08-pipelineB-spm/extractROIdata.m → scripts-09-pipelineB-spm/extractROIdata.m
diff --git a/scripts-08-pipelineB-spm/importTSVProtocol.m → scripts-09-pipelineB-spm/importTSVProtocol.m b/scripts-08-pipelineB-spm/importTSVProtocol.m → scripts-09-pipelineB-spm/importTSVProtocol.m
diff --git a/...spm/tapas_physio_read_physlogfiles_bids.m → ...spm/tapas_physio_read_physlogfiles_bids.m b/...spm/tapas_physio_read_physlogfiles_bids.m → ...spm/tapas_physio_read_physlogfiles_bids.m
diff --git a/...sub-01_ses-01_task-inhib_run-1_events.tsv → ...sub-01_ses-01_task-inhib_run-1_events.tsv b/...sub-01_ses-01_task-inhib_run-1_events.tsv → ...sub-01_ses-01_task-inhib_run-1_events.tsv
diff --git a/...sub-01_ses-01_task-inhib_run-2_events.tsv → ...sub-01_ses-01_task-inhib_run-2_events.tsv b/...sub-01_ses-01_task-inhib_run-2_events.tsv → ...sub-01_ses-01_task-inhib_run-2_events.tsv
diff --git a/...sub-01_ses-01_task-inhib_run-3_events.tsv → ...sub-01_ses-01_task-inhib_run-3_events.tsv b/...sub-01_ses-01_task-inhib_run-3_events.tsv → ...sub-01_ses-01_task-inhib_run-3_events.tsv
diff --git a/...sub-01_ses-01_task-inhib_run-4_events.tsv → ...sub-01_ses-01_task-inhib_run-4_events.tsv b/...sub-01_ses-01_task-inhib_run-4_events.tsv → ...sub-01_ses-01_task-inhib_run-4_events.tsv
diff --git a/...sub-01_ses-01_task-inhib_run-5_events.tsv → ...sub-01_ses-01_task-inhib_run-5_events.tsv b/...sub-01_ses-01_task-inhib_run-5_events.tsv → ...sub-01_ses-01_task-inhib_run-5_events.tsv
diff --git a/...sub-01_ses-01_task-inhib_run-6_events.tsv → ...sub-01_ses-01_task-inhib_run-6_events.tsv b/...sub-01_ses-01_task-inhib_run-6_events.tsv → ...sub-01_ses-01_task-inhib_run-6_events.tsv