update README

Author: Remi-Gau

README.md

@@ -57,7 +57,6 @@ as a submodule, and intitialized when running `initCppSpm`.
 
 ### Dependencies
 
-<<<<<<< HEAD
 =======
 TODO
 
@@ -101,9 +100,6 @@ Also includes:
 -   Yeo's 7 networks "atlas"
     -   add REF and URL
 
->>>>>>> 4a2a3830905dfad9b61804bf99e2941a49e4e2fa
-
-
 ## Contributing
 
 ## Contributors

demos/roi/step_7_get_ROI_PSC.m

@@ -0,0 +1,189 @@
+% This script will run through the ROIs made for each subject fo a ROI
+% based anaylisis using MarsBar to get a time course of the activations and
+% a percent signal change for each ROI and subject
+
+clc;
+
+if ~exist('machine_id', 'var')
+  machine_id = 2; % 0: container ;  1: Remi ;  2: Beast
+end
+
+% 'MNI' or  'T1w' (native)
+if ~exist('space', 'var')
+  space = 'T1w';
+end
+
+if ~exist('randomize', 'var')
+  randomize = 0;
+end
+
+% event specification for getting fitted event time-courses
+contrast_idx = 1;
+event_session_no = repmat(1:4, 1, 4);
+event_type_no = repmat([1:4]', 1, 4)';
+event_spec = [event_session_no; event_type_no(:)'];
+event_duration = 16; % default SPM event duration
+
+% FOR INFO
+% contrast_ls = {
+%     'Euc-Left + Alm-Left + Euc-Right + Alm-Right > 0'
+%     'Euc-Left + Alm-Left + Euc-Right + Alm-Right < 0'
+%     'Alm-Left + Alm-Right > 0'
+%     'Alm-Left + Alm-Right < 0'
+%     'Euc-Left + Euc-Right > 0'
+%     'Euc-Left + Euc-Right < 0'
+%     'Euc-Right + Alm-Right > 0'
+%     'Euc-Right + Alm-Right < 0'
+%     'Euc-Left + Alm-Left > 0'
+%     'Euc-Left + Alm-Left < 0'
+%     'Euc-Left > 0'
+%     'Euc-Left < 0'
+%     'Alm-Left > 0'
+%     'Alm-Left < 0'
+%     'Euc-Right > 0'
+%     'Euc-Right < 0'
+%     'Alm-Right > 0'
+%     'Alm-Right < 0'
+%     'resp-03 + resp-12 > 0'
+%     'resp-03 + resp-12 < 0'};
+
+%%
+% setting up directories
+[data_dir, code_dir, output_dir, fMRIprep_DIR] = set_dir(machine_id);
+
+% Set up the SPM defaults, just in case
+addpath(fullfile(spm('dir'), 'toolbox', 'marsbar'));
+% Start marsbar to make sure spm_get works
+marsbar('on');
+
+% get data info
+bids =  spm_BIDS(fullfile(data_dir, 'raw'));
+
+% get subjects
+folder_subj = get_subj_list(output_dir);
+folder_subj = cellstr(char({folder_subj.name}')); % turn subject folders into a cellstr
+[~, ~, folder_subj] = rm_subjects([], [], folder_subj, true);
+nb_subjects = numel(folder_subj);
+group_id = ~cellfun(@isempty, strfind(folder_subj, 'ctrl')); %#ok<*STRCLFH>
+
+% see what GLM to run
+opt = struct();
+[sets] = get_cfg_GLMS_to_run();
+[opt, all_GLMs] = set_all_GLMS(opt, sets);
+
+if randomize
+  shuffle_subjs = randperm(length(group_id));
+end
+
+%% for each subject
+
+time_course = {};
+percent_signal_change = {};
+
+for i_subj = 1:nb_subjects
+
+  fprintf('running %s\n', folder_subj{i_subj});
+
+  subj_dir = fullfile(output_dir, [folder_subj{i_subj}]);
+
+  roi_src_folder = fullfile(data_dir, 'derivatives', 'ANTs', folder_subj{i_subj}, 'roi');
+  if strcmp(space, 'MNI')
+    roi_src_folder = fullfile(code_dir, 'inputs');
+  end
+
+  roi_tgt_folder = fullfile(subj_dir, 'roi');
+  mkdir(roi_tgt_folder);
+
+  marsbar_save_folder = fullfile(output_dir, '..', 'marsbar', folder_subj{i_subj});
+  mkdir(marsbar_save_folder);
+
+  % list ROIs
+  roi_ls =  spm_select('FPList', ...
+                       roi_src_folder, ...
+                       ['^ROI-.*_space-' space '.nii$']);
+  roi_ls = cellstr(roi_ls);
+
+  % go through all the models specified and get for each ROI the percetn
+  % signal change and time course
+  fprintf(' running GLMs\n');
+  for i_GLM = 1:size(all_GLMs)
+
+    cfg = get_configuration(all_GLMs, opt, i_GLM);
+
+    cfg_list{i_GLM} = cfg;
+
+    % directory for this specific analysis
+    analysis_dir = name_analysis_dir(cfg, space);
+    analysis_dir = fullfile ( ...
+                             output_dir, ...
+                             folder_subj{i_subj}, 'stats', analysis_dir);
+
+    SPM = load(fullfile(analysis_dir, 'SPM.mat'));
+
+    for i_roi = 1:size(roi_ls, 1)
+
+      roi = roi_ls{i_roi};
+
+      [path, file] = spm_fileparts(roi);
+
+      img = spm_read_vols(spm_vol(roi));
+
+      disp(sum(img(:) > 0));
+
+      % create ROI object for Marsbar and convert to matrix format to avoid delicacies of image format
+      roi_obj = maroi_image(struct('vol', spm_vol(roi), 'binarize', 1, ...
+                                   'func', []));
+      roi_obj = maroi_matrix(roi_obj);
+
+      % give it a label
+      label(roi_obj, strrep(file, 'ROI-', ''));
+      saveroi(roi_obj, fullfile(roi_tgt_folder, [file '_roi.mat']));
+
+      D = mardo(SPM);
+
+      try
+
+        % Extract data
+        Y = get_marsy(roi_obj, D, 'mean');
+
+        % MarsBaR estimation
+        E = estimate(D, Y);
+
+        % Get, store statistics
+        stat_struct = compute_contrasts(E, contrast_idx);
+
+        % And fitted time courses
+        [tc, dt] = event_fitted(E, event_spec, event_duration);
+
+        % Get percent signal change
+        psc = event_signal(E, event_spec, event_duration, 'abs max');
+
+        % Make fitted time course into ~% signal change
+        block_means(E);
+        tc = tc / mean(block_means(E)) * 100;
+
+        % Store values
+        time_course{i_roi, i_GLM}(i_subj, :) = tc; %#ok<SAGROW>
+        percent_signal_change{i_GLM}(i_subj, i_roi) = psc;
+
+        % sqve for this subject, ROI, GLM
+        name_save_file = fullfile(marsbar_save_folder, ...
+                                  [file '_' name_analysis_dir(cfg, space) '.mat']);
+        save(name_save_file, 'tc', 'psc', 'cfg', 'file', 'dt');
+
+      catch
+
+        warning('\n\nSomething went wrong: %s - %s\n\n', ...
+                folder_subj{i_subj}, file);
+
+      end
+
+    end
+  end
+
+  if randomize
+    time_course{i_roi, i_GLM} = time_course{i_roi, i_GLM}(shuffle_subjs, :);
+    percent_signal_change{i_GLM} = percent_signal_change{i_GLM}(shuffle_subjs);
+  end
+
+end