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completedprojects:eegsnr [2024/12/02 10:07] – sdm63completedprojects:eegsnr [2025/05/06 13:09] (current) – sdm63
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 == Code Documentation ==  == Code Documentation == 
   * Preprocessing   * Preprocessing
-    * Preprocessing can be run using [[https://github.com/LabNeuroCogDevel/7T_EEG/blob/main/Cortical_SNR_Development/01_Cortical_SNR_Preprocessing.sh|01_Cortical_SNR_Preprocessing.sh]]+    * Preprocessing can be run using [[https://github.com/LabNeuroCogDevel/Cortical_SNR_Development/blob/main/01_Cortical_SNR_Preprocessing.sh|01_Cortical_SNR_Preprocessing.sh]]
     * <code> matlab -nodesktop -r "addpath(genpath('../Preprocessing_Functions/')); run_preprocessing_pipeline('SNR')" </code>     * <code> matlab -nodesktop -r "addpath(genpath('../Preprocessing_Functions/')); run_preprocessing_pipeline('SNR')" </code>
       * Pulls in raw data from hera('Raw/EEG/7TBrainMech')       * Pulls in raw data from hera('Raw/EEG/7TBrainMech')
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   * Calculate Total, Evoked, and Spontaneous Activity   * Calculate Total, Evoked, and Spontaneous Activity
-    * Run the bash script [[https://github.com/LabNeuroCogDevel/7T_EEG/blob/main/Cortical_SNR_Development/02_CreateIndividualSubjectFiles_EvokedSpontaneous.sh|02_CreateIndividualSubjectFiles_EvokedSpontaneous.sh]]+    * Run the bash script [[https://github.com/LabNeuroCogDevel/Cortical_SNR_Development/blob/main/02_CreateIndividualSubjectFiles_EvokedSpontaneous.sh|02_CreateIndividualSubjectFiles_EvokedSpontaneous.sh]]
     * <code> matlab -nodesktop -r "addpath(genpath('code/')); totalEvokedSpontaneous('4')" </code>     * <code> matlab -nodesktop -r "addpath(genpath('code/')); totalEvokedSpontaneous('4')" </code>
       * Calls totalEvokedSpontaneous.m (Cortical_SNR_Deveopment/code)       * Calls totalEvokedSpontaneous.m (Cortical_SNR_Deveopment/code)
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   * Combine Individual Subject Files   * Combine Individual Subject Files
-    * [[https://github.com/LabNeuroCogDevel/7T_EEG/blob/main/Cortical_SNR_Development/03_CombineSubDataframes.R|03_CombineSubDataframes.R]]+    * [[https://github.com/LabNeuroCogDevel/Cortical_SNR_Development/blob/main/03_CombineSubDataframes.R|03_CombineSubDataframes.R]]
     * <code>     * <code>
 #!/usr/bin/env Rscript #!/usr/bin/env Rscript
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   * Combine All Stimulus Conditions   * Combine All Stimulus Conditions
-    * [[https://github.com/LabNeuroCogDevel/7T_EEG/blob/main/Cortical_SNR_Development/04_combineAllStimConditions.R|04_combineAllStimConditions.R]]+    * [[https://github.com/LabNeuroCogDevel/Cortical_SNR_Development/blob/main/04_combineAllStimConditions.R|04_combineAllStimConditions.R]]
       * Combines the csv files on the previous step into one large csv files with all frequency stimulus conditions       * Combines the csv files on the previous step into one large csv files with all frequency stimulus conditions
       * Preforms outlier detection (2 SDs above the mean)       * Preforms outlier detection (2 SDs above the mean)
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   * Impute missing data and Calculate frontal region PCA   * Impute missing data and Calculate frontal region PCA
-    * [[https://github.com/LabNeuroCogDevel/7T_EEG/blob/main/Cortical_SNR_Development/05_createImputed_PCA_dataFrames.R|05_createImputed_PCAdataframes.R]]+    * [[https://github.com/LabNeuroCogDevel/Cortical_SNR_Development/blob/main/05_createImputed_PCA_dataFrames.R|05_createImputed_PCAdataframes.R]]
       * Read in csv with all subjects info        * Read in csv with all subjects info 
       * Select the freq and hertz combo you want to analyze       * Select the freq and hertz combo you want to analyze
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   * Figures and Statistics   * Figures and Statistics
-    * [[https://github.com/LabNeuroCogDevel/7T_EEG/blob/main/Cortical_SNR_Development/06_SNR_Results.Rmd| 06_SNR_Results.Rmd]]+    * [[https://github.com/LabNeuroCogDevel/Cortical_SNR_Development/blob/main/06_SNR_Results.Rmd| 06_SNR_Results.Rmd]]
     * To assess developmental trajectories of cortical SNR activity, we implemented GAMMs on the first principal component, PC1, of evoked power, spontaneous power, and SNR, including random intercepts estimated for each participant.      * To assess developmental trajectories of cortical SNR activity, we implemented GAMMs on the first principal component, PC1, of evoked power, spontaneous power, and SNR, including random intercepts estimated for each participant. 
     * Regression splines were implemented (4 degrees of freedom) to assess linear and non-linear effects.      * Regression splines were implemented (4 degrees of freedom) to assess linear and non-linear effects.