/PROSOCIAL

PROS are the Matlab and R scripts for the analysis of PROS project

Primary LanguageR

PROS

PROS scripts are the Matlab and R scripts for the analysis of PROS(Age differences in prosocial decision making) project 2017 Z.Y.C. . Matlab for brain image analysis(using SPM12 package), and R for behavioral analysis.

raw data processing:

  • Sign into the root

  • Rsync NCCUFTP to your own directory :

rsync -avhr myfile.gz /home/pi/tmp/
  • Change the owner authority:
chown -R kevincayenne:kevincayenne

  • Exit the root

  • Creat the directories:

    1. Converted_files
    2. tryFIR

  • Unzip nii files:

dcm2nii -d N -g N -o /bml/Data/Bank5/PROS//Pilot_image/Convert_data/PROS-Pilot-4 /bml/Data/Bank5/PROS/Pilot_image/RAW_image/PROS-PILOT-4

behavior analysis procedure:

  • Behavior analysis R file:
data_merge

spm fMRI analysis procedure:

  1. preprocessing script

  2. first_level_generate_matfile script -> generate SOA.mat for first level (just do once)
    * before run the file:

    1. transport the behavior.csv to the server

    2. combine txt files into combinedtxt.txt
      * cat rp_aep2dmoco4mm181A* rp_aep2dmoco4mm181B* rp_aep2dmoco4mm181C* rp_aep2dmoco4mm181D* rp_aep2dmoco4mm181E* rp_aep2dmoco4mm151F* > combinedtxt.txt

  3. firstlevel_FIR script -> without estimate
    * % motion orthogonalize: spm_fmri_concatenate(target_output_spm, scans);

  4. covariance script -> generate the .mat file for second level script

  5. second level script -> generate design matrix for first level

    1. % delete first column: SPM.xX.X(:,1) = [];

    2. % change '19' to '1': SPM.xX.X(SPM.xX.X(:,:)==19) = 1;

  6. firstlevel model estimate script -> model estimate for first level matrix

  7. firstlevel_contrast script -> generate F-contrasts and T-contrast for group level analysis

  8. secondlevel_group_analysis -> generate group design matrix and estiamte

  9. secondlevel_group_contrast -> group contrast

  10. group_contrast_masking -> add mask to each Tcon file

  11. group_3D_to_4D -> combine 3D 12 time courses contrast to 4D contrast