From e9dbcf288f7c34e08ee281f9b47e94819b9411b1 Mon Sep 17 00:00:00 2001 From: Jingxuan Gong Date: Fri, 21 Oct 2022 12:48:08 -0500 Subject: [PATCH] Update README.md --- README.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index ab03e1f..10b4519 100644 --- a/README.md +++ b/README.md @@ -70,7 +70,7 @@ __Outputs__ For analysis of amplitude threshold **bands**, [CorrelationBand_Calc.m](CorrelationBand_Calc.m) was run, and the inputs and outputs match what is described above. An additional output (for less-smoothed Rapidtide outputs only) is a MATLAB data file of group median values of slope, correlation coefficient (Z-transformed), and voxel percentage remaining for each amplitude threshold band. This is for the use of comparing with additionally smoothed Rapidtide outputs in plots. -#### 1B) [Correlation_Subject-Scatterplots.m](Correlation_Subject-Scatterplots.m) (datatypes,restlag,tasklag,mask_inputdir,mask_prefix,outputdir,subject_list) +#### 1B) [Correlation_Subject_Scatterplots.m](Correlation_Subject_Scatterplots.m) (datatypes,restlag,tasklag,mask_inputdir,mask_prefix,outputdir,subject_list) This function produces a graphical representation of the previous step, therefore can be done independently of the previous step and is not required for later analysis. @@ -83,9 +83,9 @@ __Outputs__ - Scatterplot of the relationship between delay times (task plotted against rest) at different amplitude thresholds, with regression lines of best fit - Only shows representative amplitude thresholds of: all GM (no threshold), 0, 0.4, maximum threshold with unique regression fitting (0.6 for CDB sub-06, 0.7 for others) -For analysis of amplitude threshold **bands**, [CorrelationBand_Subject-Scatterplots.m](CorrelationBand_Subject-Scatterplots.m) was run, and the inputs and outputs match what is described above. Representative amplitude threshold bands are plotted: 0-0.2, 0.2-0.4, 0.4-0.6. +For analysis of amplitude threshold **bands**, [CorrelationBand_Subject_Scatterplots.m](CorrelationBand_Subject_Scatterplots.m) was run, and the inputs and outputs match what is described above. Representative amplitude threshold bands are plotted: 0-0.2, 0.2-0.4, 0.4-0.6. -#### 1C) [Correlation_Group-Boxplots.m](Correlation_Group-Boxplots.m) (datatypes,inputdir,outputdir,corrthres) +#### 1C) [Correlation_Group_Boxplots.m](Correlation_Group_Boxplots.m) (datatypes,inputdir,outputdir,corrthres) This function generates group summary plots based on the outputs of (1A). @@ -95,13 +95,13 @@ __Inputs__ __Outputs__ - Boxplots of group average slope, correlation coefficient (Z-transformed), intercept, and voxel percentage remaining -For analysis of amplitude threshold **bands**, [CorrelationBand_Group-Boxplots.m](CorrelationBand_Group-Boxplots.m) was run, and the inputs and outputs match what is described above. For additionally smoothed outputs, the less-smoothed outputs are overlaid for ease of comparison. +For analysis of amplitude threshold **bands**, [CorrelationBand_Group_Boxplots.m](CorrelationBand_Group_Boxplots.m) was run, and the inputs and outputs match what is described above. For additionally smoothed outputs, the less-smoothed outputs are overlaid for ease of comparison. ### Part 2. GM voxels in specific subregions (parcels) This part was run on the BH+REST dataset (less-smoothed inputs only). -#### 2A) [Parcel-Correlation_Calc.m](Parcel-Correlation_Calc.m) (restlag,tasklag,mask_inputdir,mask_prefix,outputdir,subject_list) +#### 2A) [Parcel_Correlation_Calc.m](Parcel_Correlation_Calc.m) (restlag,tasklag,mask_inputdir,mask_prefix,outputdir,subject_list) This function is the same as (1A-Correlation_Calc.m) but performs the correlation seperately for each GM subregion. @@ -114,22 +114,22 @@ __Outputs__ - Excel sheets and .mat files recording the correlation between delay times at different amplitude thresholds, for future group average analysis and plotting - These files are important for generating group average boxplots -#### 2B) [Parcel-Correlation_Group-PerPlot.m](Parcel-Correlation_Group-PerPlot.m) (inputdir,outputdir,corrthres) +#### 2B) [Parcel_Correlation_Group_PerPlot.m](Parcel_Correlation_Group_PerPlot.m) (inputdir,outputdir,corrthres) This function plots the percentage of voxels passing the amplitude threshold in task and rest data segments, using outputs from 2A (Parcel-Correlation_Calc.m) __Inputs__ -- Parcel-Correlation_Calc.m outputs - Excel sheets and .mat files +- Parcel_Correlation_Calc.m outputs - Excel sheets and .mat files __Outputs__ - A plot of median voxel percentage passing each amplitude threshold, across all subjects. Each colored line represents a different GM parcel with the entire GM as a black line. -#### 2C) [Parcel-Correlation_Group-Others.m](Parcel-Correlation_Group-Others.m) (inputdir,outputdir,corrthres) +#### 2C) [Parcel_Correlation_Group_Others.m](Parcel_Correlation_Group_Others.m) (inputdir,outputdir,corrthres) This function plots the slope and r (Z-transformed) from the task vs. rest delay regression, using outputs from 2A (Parcel-Correlation_Calc.m) __Inputs__ -- Parcel-Correlation_Calc.m outputs - Excel sheets and .mat files +- Parcel_Correlation_Calc.m outputs - Excel sheets and .mat files __Outputs__ - A plot of median slope and median r (Z-transformed) for each amplitude threshold, across all subjects. Each colored line represents a different GM parcel with the entire GM as a black line.