Added SPM scripts

3_experiment/3_3_data_analysis_fr/spm/UTSC_cluster_wrapper.m

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+function UTSC_cluster_wrapper(varargin)
+% function UTSC_cluster_wrapper([modelID],[numworkers],[startSubj])
+%
+% Function for submitting a single-subject GLM analysis to be run
+% on the computing cluster at UTSC.
+%
+% If submitted with no arguments, will prompt the user for the model ID, 
+% the number of nodes/workers to use, and the subject ID to start with
+%
+% Can also be run as a function, submitting the following optional
+% arguments:
+% modelID (e.g. '1_Preference'): a string identifying the name of the model
+% - if calling as a function, modelID is a mandatory argument
+% 'NumWorkers', followed by a number, indicating nodes to be used (default:
+% 12)
+% 'startSubj', followed by starting index of subject: a variable that
+% allows you to skip some subjects and start later in the list
+
+    pathtofile = mfilename('fullpath');
+    homepath = pathtofile(1:(regexp(pathtofile,'derivatives')-1));
+
+    addpath(fullfile(homepath, 'derivatives','spm','code'))
+
+    % if called with arguments, use them, otherwise get them from user
+    if isempty(varargin)
+        model = input('Which model to run?: ', 's');
+        numWorkers = input('How many workers to request?: ');
+        startID = input('Which subject to start with?: ');
+    else 
+        model = varargin{1};
+        if length(varargin) > 1
+            numWorkers = varargin{2};
+        else 
+            numWorkers = 12;
+        end
+
+        if length(varargin) > 2
+            startID = varargin{3};
+        else
+            startID = 1;
+        end
+    end
+
+    if isempty(numWorkers)
+        numWorkers = 12;
+    end
+
+    if isempty(startID)
+        startId = 1;
+    end
+
+    %% get subject info and create submission info for each node
+    cd(homepath)
+
+%     load(fullfile('derivatives', 'spm','code','subject_list.mat')); % subject IDs for each study
+
+    subject_list; % creates subject list variables
+
+    numSubjects = length(good_subjects.subjects);
+
+    %% schedule tasks
+    clu=parcluster('default_jobmanager');
+
+    pjob=createJob(clu,'RestartWorker',logical(1),'NumWorkersRange', [1,  numWorkers]);
+    set(pjob,'AdditionalPaths',{...
+        fullfile(homepath,'derivatives','spm','code'),...
+        '/psyhome/u7/hutchers/matlabextras/', ...
+        ['/psyhome/u5/wilso603/Matlab/spm8']})
+
+    for s = startID:numSubjects
+         eval(['createTask(pjob, @' ...
+               ['foodreg_m' model '_analyze2']...
+               ', 0 ,{''' all_subjects.subjects{s} '''},''MaximumRetries'',50);'])
+    end
+    t = get(pjob,'Tasks');
+    submit(pjob)
+
+    %% start monitoring job progress
+% 
+%     results = fetchOutputs(pjob);
+% 
+%     %% check for errors
+%     nErrors = 0;
+%     idError = [];
+%     for i = 1:length(t)
+%         if ~isempty(t(i).ErrorMessage)
+%             nErrors = nErrors+1;
+%             idError = [idError i];
+%         end
+%     end
+% 
+%     %% housecleaning: delete job info if no errors
+%     if nErrors == 0    
+%         dirname = pjob.Name;
+%         pause(2)
+%         unix(['rm -r ' homepath 'jobdata/' dirname '*']);
+%         fprintf('\nJob successfully completed.\n\n')
+%     else
+%         fprintf('Errors were detected! History of first error: \n\n')
+%         t(idError(1))
+%     end
+% 
+%     finished_jobs = findJob(clu,'State','finished','Username','hutchers');
+%     delete(finished_jobs);

3_experiment/3_3_data_analysis_fr/spm/batch_run.m

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+
+% ANALYZE
+% foodreg_m1_Preference_analyze2(new_subjects.subjects, 'SubjectData_icaAroma_nonAggr_6mm')
+% foodreg_m1_PostPre_analyze2(new_subjects.subjects, 'SubjectData_icaAroma_nonAggr_6mm')
+% foodreg_m1_TasteHealth_analyze2(new_subjects.subjects, 'SubjectData_icaAroma_nonAggr_6mm')
+% 
+% foodreg_m1_Preference_analyze2(new_subjects.subjects, 'SubjectData_MNI152_8mm')
+% foodreg_m1_PostPre_analyze2(new_subjects.subjects, 'SubjectData_MNI152_8mm')
+% foodreg_m1_TasteHealth_analyze2(new_subjects.subjects, 'SubjectData_MNI152_8mm')
+% foodreg_m4_preference_a_pre_m_post_analyze2(good_subjects.subjects, 'SubjectData_MNI152_8mm')
+% foodreg_m5_preference_a_reg_success_lasting_analyze2(good_subjects.subjects, 'SubjectData_MNI152_8mm')
+% foodreg_m7_preference_a_reg_success_lasting_post_trial_analyze2(remaining_subjects.subjects, 'SubjectData_MNI152_8mm')
+% foodreg_m8_pre_liking_analyze2(remaining_subjects.subjects, 'SubjectData_MNI152_8mm')
+
+% CONTRASTS
+preproc_version = 'SubjectData_MNI152_8mm';
+% 
+% contrast2_par_m1_preference(good_subjects.subjects, preproc_version);
+% contrast2_par_m2_taste_a_health(good_subjects.subjects, preproc_version);
+% contrast2_par_m3_pre_m_post(good_subjects.subjects, preproc_version);
+% contrast2_par_m4_preference_a_pre_m_post(good_subjects.subjects, preproc_version);
+% contrast2_par_m5_preference_a_reg_success_lasting(good_subjects.subjects, preproc_version);
+% contrast2_par_m7_preference_a_reg_success_lasting_post_trial(good_subjects.subjects, preproc_version);
+% contrast2_par_m8_pre_liking(good_subjects.subjects, preproc_version);
+
+
+% 2ND LEVEL
+% cd /Volumes/DJW_Lacie_01/PROJECTS/2018_Food_Reg_fMRI/09_DATA/food_reg_fmri_01/analysis/SPM/
+% f = fullfile('m1_Preference', preproc_version, 'm1_Preference_cons.mat');
+% load(f);
+% for con = 1:length(cname)
+% rfx_par('m1_Preference',cname(con),good_subjects,preproc_version)
+% end
+% 
+% cd /Volumes/DJW_Lacie_01/PROJECTS/2018_Food_Reg_fMRI/09_DATA/food_reg_fmri_01/analysis/SPM/
+% f = fullfile('m2_taste_a_health', preproc_version, 'm2_taste_a_health_cons.mat');
+% load(f);
+% for con = 1:length(cname)
+% rfx_par('m2_taste_a_health',cname(con),good_subjects,preproc_version)
+% end
+% 
+% cd /Volumes/DJW_Lacie_01/PROJECTS/2018_Food_Reg_fMRI/09_DATA/food_reg_fmri_01/analysis/SPM/
+% f = fullfile('m3_pre_m_post', preproc_version, 'm3_pre_m_post_cons.mat');
+% load(f);
+% for con = 1:length(cname)
+% rfx_par('m3_pre_m_post',cname(con),good_subjects,preproc_version)
+% end
+
+% cd /Volumes/DJW_Lacie_01/PROJECTS/2018_Food_Reg_fMRI/09_DATA/food_reg_fmri_01/analysis/SPM/
+% f = fullfile('7_preference_a_reg_success_lasting_post_trial', preproc_version, 'm7_preference_a_reg_success_lasting_post_trial_cons.mat');
+% load(f);
+% for con = 1:length(cname)
+% rfx_par('7_preference_a_reg_success_lasting_post_trial',cname(con),good_subjects,preproc_version)
+% end
+
+cd /Volumes/DJW_Lacie_01/PROJECTS/2018_Food_Reg_fMRI/09_DATA/food_reg_fmri_01/analysis/SPM/
+f = fullfile('8_pre_liking', preproc_version, 'm8_pre_liking_cons.mat');
+load(f);
+for con = 1:length(cname)
+rfx_par('8_pre_liking',cname(con),good_subjects,preproc_version)
+end