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MOT_ANA/Script_Motion.m
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Script_Motion.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Authors: Thomas Bolton and Mert Inan
% Date: 03/08/2017 -
% Description:
% This script will perform classical preprocessing steps on the HCP data in
% order to analyse it in different ways:
%
% - Through regional sparse coupled hidden Markov models
% - Through co-activation pattern analysis
% - Through variance-related assessment of motion
% - Through Total activation on graphs
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% 1. Setting up path files
% Adds the shared folder to do all we want: contains SPM8
PathSPM = '/media/miplab-nas3/Code-NAS1/shared/static_FC_pipeline/spm8';
PathPrepro = '/media/miplab-nas3/Code-NAS1/projects/ABIDE/preprocessing_Thomas/MyPreprocessing';
PathDPARSFA = '/media/miplab-nas3/Code-NAS1/shared/static_FC_pipeline/DPARSF_V2.3_130615';
% If the 'server link' exists, we add the path. Else, we add the computer
% path (with Volumes)
try
addpath(genpath(PathSPM));
catch
addpath(genpath('/Volumes/Code-NAS1/shared/static_FC_pipeline/spm8'));
end
try
addpath(genpath(PathPrepro));
catch
addpath(genpath('/Volumes/Code-NAS1/projects/ABIDE/preprocessing_Thomas/MyPreprocessing'));
end
try
addpath(genpath(PathDPARSFA));
catch
addpath(genpath('/Volumes/Code-NAS1/shared/static_FC_pipeline/DPARSF_V2.3_130615'));
end
% ------------- DATA PATH TO READ FROM -------------
% **** Changed from /media/miplab-nas2/data/HCP_Data_TA' ****
% Need to check that writing to this path is not done!
readPath = '/media/miplab-nas3/HCP-Data/HCP_Giulia';
%readPath = '/Volumes/HCP-Data/HCP_Giulia';
% ------------- DATA PATH TO WRITE TO -------------
writePath = '/Users/TiBiUan/Desktop/Github/MOT_ANA';
%writePath = '/Volumes/Data/Regional_SCHMM';
%% 2. Setting up options
% We change directory towards where we store the RS data
cd(readPath);
% Choose the wave of the subjects
wave = '1st_wave_90subjs'; %Change loop cycle count when you change this
wave ='2nd_wave_158subjs';
% Indices of the subjects to preprocess
pathToSubjectsFunc = fullfile(readPath, 'Preproc_sFC', wave);
d = dir(pathToSubjectsFunc);
d = d(4:end,:);
% Type of acquisition for the subjects (RL or LR): for this data, we only
% have the LR session available for now
d2 = 'rfMRI_REST1_LR';
%d2 = 'rfMRI_REST1_RL';
% Number of scans to remove
removeFirstNscans = 10;
%% 3. Preprocessing itself
% I iterate through all the HCP folders and create respective folders in
% the write directory
for i = 1:135
try
disp(['Subject ',d(i).name,'...']);
%Creating a folder in the write directory
if isequal(d2,'rfMRI_REST1_RL')
writeFolder = [d(i).name,'_RL']; %Change according to d2
else
writeFolder = d(i).name;
end
cd(writePath);
mkdir(writeFolder);
cd(writeFolder);
%mkdir('Structural');
mkdir('Motion');
cd(readPath);
% READ Structural and functional paths
%structPath = fullfile(pathToSubjectsStruct,d(i).name,'T1');
functPath = fullfile(pathToSubjectsFunc,d(i).name,'fMRI');
% WRITE Structural and functional paths
%structWritePath = fullfile(writePath,writeFolder,'Structural');
functWritePath = fullfile(writePath,writeFolder);
% Reads and modifies the text file to have 594 rows and to have proper
% units, then copies it from read location to write location.
movText = textread(fullfile(functPath,'rp_Movement_Regressors.txt'));
%Changes degrees to radians
movText = movText(:,1:6);
for l = 4:6
movText(:,l) = movText(:,l)*pi/180;
end
dlmwrite(fullfile(functWritePath,'Motion','Movement_Regressors.txt'),movText,' ');
catch
warning(['Could not do it for the ',int2str(i), '. iteration.']);
continue;
end
end
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