add readme's, tidy up

CIBIT-UC · Jul 15, 2023 · ff9577e · ff9577e
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diff --git a/legacy/FiguresPaper_1_psc.png b/legacy/FiguresPaper_1_psc.png
diff --git a/legacy/FiguresPaper_1_psc2static.png b/legacy/FiguresPaper_1_psc2static.png
diff --git a/legacy/FiguresPaper_2_psc.png b/legacy/FiguresPaper_2_psc.png
diff --git a/legacy/FiguresPaper_2_psc2static.png b/legacy/FiguresPaper_2_psc2static.png
diff --git a/legacy/GroupERA_N20_BilateralMT_D0_2MotionBlock.png b/legacy/GroupERA_N20_BilateralMT_D0_2MotionBlock.png
diff --git a/legacy/GroupERA_N20_BilateralMT_D0_2MotionBlock_psc2static.png b/legacy/GroupERA_N20_BilateralMT_D0_2MotionBlock_psc2static.png
diff --git a/legacy/GroupERA_N20_BilateralMT_D0_FullTrial_psc.png b/legacy/GroupERA_N20_BilateralMT_D0_FullTrial_psc.png
diff --git a/legacy/GroupERA_N20_BilateralMT_D0_FullTrial_psc2static.png b/legacy/GroupERA_N20_BilateralMT_D0_FullTrial_psc2static.png
diff --git a/scripts-04-eyetracker/README.md b/scripts-04-eyetracker/README.md
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+# scripts-04-eyetracker
+Scripts to analyze the eye-tracking data.
diff --git a/scripts-05-pipelineA-analysis/README.md b/scripts-05-pipelineA-analysis/README.md
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+# scripts-05-pipelineA-analysis
+Scripts to estimate and display event-related responses (ERAs) from the fMRI data using SPM12.
+
+## Files:
+- `TC_Extraction.m`: extract the time courses from the ROIs based on subject-specific coordinates.
+- `ExpC_ERA_SPM.m`: subject-level script to estimate the ERAs from the extracted time courses.
+- `ExpC_ERA_SPM_Group.m`: group-level script.
+- `FiguresPaper.m`: script to generate the figures for the paper.
diff --git a/scripts-05-pipelineA-spm/README.md b/scripts-05-pipelineA-spm/README.md
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+# scripts-05-pipelineA-spm
+
+- fsleyes_visualization.md: contains the script to visualize results using FSLeyes.
diff --git a/scripts-08-pipelineB-spm/README.md b/scripts-08-pipelineB-spm/README.md
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+# scripts-08-pipelineB-spm
+
+## Files:
+- `Step01_MainSPM.m`: script to run the SPM pipeline (1st level analysis, single and multi run)
+- `Step02_ExtractTCfromROI.m`: script to extract the time course from a ROI based on spherical subject-specific coordinates and the activation map of each functional run.
+- `Step03_CalculateERAs.m`: script to calculate the event-related averages (ERAs) from the time course of each ROI. Generates the figures.
+- `Step04_ExtractTvalues.m`: script to extract the t-values from the activation map of each functional run based on spherical subject-specific coordinates.
diff --git a/tools/README.md b/tools/README.md
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+# tools
+Necessary tools for the project.
+
+- edf-converter: Eyelink format reader
+- jsonlab: JSON reader
+- shadedErrorBar: Shaded error bar plots
+- suptitle: Super title for subplots
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		# scripts-04-eyetracker
		Scripts to analyze the eye-tracking data.
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		# scripts-05-pipelineA-spm

		- fsleyes_visualization.md: contains the script to visualize results using FSLeyes.