update fLoCAnalysis and Params file to be transformed into a gear, ad…

…ded parameters to logfile

functions/fLocAnalysis.m

@@ -1,13 +1,14 @@
-function err = fLocAnalysis(session, init_params, glm_params, clip, stc)
+function err = fLocAnalysis(session, init_params, glm_params, clip, QA)
 % Automated analysis of fMRI data from fLoc funcional localizer experiment 
 % using vistasoft functions (https://github.com/vistalab/vistasoft). 
 % 
-% INPUTS
+% INPUTS fLocAnalysis(session, init_params, glm_params, clip, QA)
 % 1) session: name of session in ~/fLoc/data/ to analyze (string)
 % 2) init_params: optional preprocessing parameters (struct)
 % 3) glm_parms: optional GLM analysis parameters (struct)
 % 4) clip: optional number of TRs to clip from beginnning of each run (int)
-% 5) stc: optional flag controlling slice time correction (logical)
+% 5) QA: optional flag controlling whether analysis exists if QA checks
+% fail (logical)
 %
 % OUTPUT
 % 1) err: 1 if analysis terminated with an error, 0 if analysis completed
@@ -21,6 +22,12 @@
 % 
 % AS 8/2018
 
+% Parfiles must be organized such that like conditions that you would like
+% to be contrasted with all other conditions are grouped in twos. In other
+% words, if the localizer uses both adult and child face conditions, they
+% should be listed as, for instance, condition numbers 1 and 2, instead of
+% 2 and 3 or 1 and 4.
+% AR 09/2018
 
 %% Check inputs and get analysis parameters
 
@@ -33,37 +40,49 @@
     [~, session_id] = fileparts(session);
 end
 
-% check and set defaults for clip and stc arguements
+% check and set defaults for clip arguement
 if nargin < 4 || isempty(clip); clip = 0; end
 if rem(clip, 1) ~= 0
     fprintf('Error: clip arguement must be an integer. \n\n'); return;
 end
-if nargin < 5 || isempty(stc); stc = true; end
-if stc == 1; stc = true; end
-if stc == 0; stc = false; end
-if ~islogical(stc)
-    fprintf('Error: stc arguement must be a logical. \n\n'); return;
+
+if nargin < 6 || isempty(QA); QA = false; end
+
+if QA == 1; QA = true; end
+if QA == 0; QA = false; end
+
+if ~islogical(QA)
+    fprintf('Error: QA argument must be a logical. \n\n'); return;
 end
 
+%Move to session's folder
+cd(session)
+
 % set preprocessing parameters if not provided
 if nargin < 2 || isempty(init_params)
-    [~, init_params, dglm_params] = fLocAnalysisParams(session, clip, stc);
+    [~, init_params, dglm_params] = fLocAnalysisParams(session, clip);
 end
 
 % set GLM analysis parameters if not provided
 if nargin < 3 || isempty(glm_params)
     glm_params = dglm_params;
 end
 
+% save params
+save fLocAnalysisParams.mat init_params glm_params
+
 % apply canonical transformation to .nii.gz files
 for rr = 1:length(init_params.functionals)
+    %init_params.glmParams{rr} = glm_params;
     niftiWrite(niftiApplyCannonicalXform(niftiRead(init_params.functionals{rr})));
 end
+
 niftiWrite(niftiApplyCannonicalXform(niftiRead(init_params.inplane)));
 nii = niftiRead(init_params.functionals{1}); nslices = size(nii.data, 3);
 
 % open logfile to track progress of analysis
-lid = fopen(fullfile(session, 'fLocAnalysis_log.txt'), 'w+');
+logFileName = fullfile(session, 'fLocAnalysis_log.txt');
+lid = fopen(logFileName, 'w+');
 fprintf(lid, 'Starting analysis for session %s. \n\n', session_id);
 fprintf('Starting analysis for session %s. \n\n', session_id);
 
@@ -75,28 +94,11 @@
 fprintf('Initializing vistasoft session directory in: \n%s \n\n', session);
 setpref('VISTA', 'verbose', false); % suppress wait bar
 if exist(fullfile(session, 'Inplane'), 'dir') ~= 7
-    mrInit(init_params);
+    mrInit(init_params); %Saves mrSESSION.mat under session's folder
 end
+
 hi = initHiddenInplane('Original', 1);
 
-% do slice timing correction assuming interleaved slice acquisition
-if stc
-    fprintf(lid, 'Starting slice timing correction... \n');
-    fprintf('Starting slice timing correction... \n');
-    if ~(exist(fullfile(session, 'Inplane', 'Timed'), 'dir') == 7)
-        load(fullfile(session, 'mrSESSION'));
-        for rr = 1:length(init_params.functionals)
-            mrSESSION.functionals(rr).sliceOrder = [1:2:nslices 2:2:nslices];
-        end
-        setpref('VISTA', 'verbose', false); % suppress wait bar
-        saveSession; hi = initHiddenInplane('Original', 1);
-        hi = AdjustSliceTiming(hi, 0, 'Timed');
-        saveSession; close all;
-    end
-    fprintf(lid, 'Slice timing correction complete. \n\n');
-    fprintf('Slice timing correction complete. \n\n');
-    hi = initHiddenInplane('Timed', 1);
-end
 
 % do within-scan motion compensation and check for motion > 2 voxels
 fprintf(lid, 'Starting within-scan motion compensation... \n');
@@ -109,16 +111,28 @@
 end
 fig = openfig(fullfile(session, 'Images', 'Within_Scan_Motion_Est.fig'), 'invisible');
 L = get(get(fig, 'Children'), 'Children');
-for rr = 1:length(init_params.functionals)
-    motion_est = L{rr + 1}.YData;
-    if max(motion_est(:)) > 2
-        fprintf(lid, 'Warning -- Within-scan motion exceeds 2 voxels. \nExited analysis.');
-        fprintf('Warning -- Within-scan motion exceeds 2 voxels. \nExited analysis.');
-        fclose(lid); return;
+if QA
+    for rr = 1:length(init_params.functionals)
+        motion_est = L{rr + 1}.YData;
+        if max(motion_est(:)) > 2
+            fprintf(lid, 'Warning -- Within-scan motion exceeds 2 voxels. \n');
+            fprintf('Warning -- Within-scan motion exceeds 2 voxels. \n');
+            fprintf(lid,'Exited analysis'); 
+            fprintf('Exited analysis');
+            ffclose(lid); 
+            return; 
+        end
+        fprintf(lid,'QA checks passed for run %i. ',rr);
+        fprintf('QA checks passed for run %i. ',rr);
     end
 end
-fprintf(lid, 'Within-scan motion compensation complete. QA checks passed. \n\n');
-fprintf('Within-scan motion compensation complete. QA checks passed. \n\n');
+
+% group motion compensation scans
+hi = initHiddenInplane('MotionComp', init_params.scanGroups{1}(1));
+hi = er_groupScans(hi, init_params.scanGroups{1});
+
+fprintf(lid, 'Within-scan motion compensation complete. \n\n');
+fprintf('Within-scan motion compensation complete. \n\n');
 
 % do between-scan motion compensation and check for motion > 2 voxels
 fprintf(lid, 'Starting between-scan motion compensation... \n');
@@ -132,6 +146,7 @@
     hi = selectDataType(hi, 'MotionComp_RefScan1');
     saveSession; close all;
 end
+
 fid = fopen(fullfile(session, 'Between_Scan_Motion.txt'), 'r');
 motion_est = zeros(length(init_params.functionals) - 1, 3);
 for rr = 1:length(init_params.functionals) - 1
@@ -141,14 +156,18 @@
     motion_est(rr, 3) = str2double(ln{14});
 end
 fclose(fid);
-if max(motion_est(:)) > 2
-    fprintf(lid, 'Warning -- Between-scan motion exceeds 2 voxels. \nExited analysis.');
-    fprintf('Warning -- Between-scan motion exceeds 2 voxels. \nExited analysis.');
-    fclose(lid); return;
+if QA
+    if max(motion_est(:)) > 2
+        fprintf(lid, 'Warning -- Between-scan motion exceeds 2 voxels. \nExited analysis.');
+        fprintf('Warning -- Between-scan motion exceeds 2 voxels. \nExited analysis.');
+    	fclose(lid); return; 
+    else
+        fprintf(lid,'QA checks passed. \n\n');
+        fprintf('QA checks passed. \n\n');
+    end
 end
-fprintf(lid, 'Between-scan motion compensation complete. QA checks passed. \n\n');
-fprintf('Between-scan motion compensation complete. QA checks passed. \n\n');
-
+fprintf(lid, 'Between-scan motion compensation complete.\n\n');
+fprintf('Between-scan motion compensation complete.\n\n');
 
 %% Analyze fMRI data and generate model parameter maps
 
@@ -181,6 +200,7 @@
 hi = er_assignParfilesToScans(hi, init_params.scanGroups{1}, init_params.parfile);
 saveSession; close all;
 
+
 % run GLM and compute default statistical contrasts
 fprintf(lid, 'Performing GLM analysis for %s... \n\n', session);
 fprintf('Performing GLM analysis for %s... \n\n', session);
@@ -206,8 +226,46 @@
 fprintf(lid, 'GLM parameter maps saved in: \n%s/GLMs/... \n\n', session);
 fprintf('GLM parameter maps saved in: \n%s/GLMs/... \n\n', session);
 
-fprintf(lid, 'fLocAnalsis for %s is complete! \n', session_id);
-fprintf('fLocAnalsis for %s is complete! \n', session_id); fclose(lid);
+fprintf(lid, 'fLocAnalsis for %s is complete! \n\n', session_id);
+fprintf('fLocAnalsis for %s is complete! \n', session_id); 
+
+% add MATLAB and Mr Vista Version to logfile 
+fprintf(lid,['---------------------------------------------------','\n\n']);
+
+fprintf(lid,['MATLAB version ',version,'\n\n']);
+load mrSESSION.mat
+fprintf(lid,['mrVista Version ',mrSESSION.mrVistaVersion,'\n\n']);
+
+% add all parameters used to logfile
+fprintf(lid,['---------------------------------------------------','\n\n']);
+
+load mrInit_params.mat
+% initialization params
+fprintf(lid,['Initialization parameters used\n\n',evalc('disp(params)')]);
+fprintf(lid,['including: functionals\n\n',evalc('disp(params.functionals(:))')]);
+fprintf(lid,['keepFrames\n\n',evalc('disp(params.keepFrames)')]);
+fprintf(lid,['parfiles\n\n',evalc('disp(params.parfile(:))')]);
+
+fprintf(lid,['---------------------------------------------------','\n\n']);
+
+% scan params
+for l = 1:length(dataTYPES(1).scanParams), fprintf(lid,['Original data type scan ',num2str(l),' params:\n\n',l,evalc( 'disp(dataTYPES(1).scanParams(l))' )]), end
+
+fprintf(lid,['GLM data type scan params:\n\n',evalc('disp(dataTYPES(4).scanParams)')]);
+
+fprintf(lid,['---------------------------------------------------','\n\n']);
+
+% GLM params
+fprintf(lid,['Event analysis parameters used\n\n',evalc('disp(dataTYPES(length(dataTYPES)).eventAnalysisParams)')]);
+
+% close file
+fclose(lid);
 err = 0;
 
+%Move cd back to fLoc from session
+cd ..
+
+%Clear workspace
+clearvars -except err
+
 end

functions/fLocAnalysisParams.m

@@ -1,11 +1,11 @@
-function [session, init_params, glm_params] = fLocAnalysisParams(session, clip, stc)
+function [session, init_params, glm_params] = fLocAnalysisParams(session, clip)
 % Generate data structures of vistasoft parameters for preprocessing and 
 % analyzing fLoc data with a GLM. 
 %
 % INPUTS
 % 1) session: name of session in ~/fLoc/data/ to analyze (string)
 % 2) clip: number of TRs to clip from beginnning of each run (int)
-% 3) stc: flag controlling slice time correction (logical)
+
 % 
 % OUPUTS
 % 1) session -- name of session in ~/fLoc/data/ to analyze (string)
@@ -26,6 +26,7 @@
 % find paths to fMRI data and corresponding stimulus parfiles
 [~, session_id] = fileparts(session);
 niifiles = dir(fullfile(session, '*.nii.gz')); niifiles = {niifiles.name};
+niifiles = niifiles(~contains(niifiles,'._')); % Alex made an edit: some file names had a random ._ at the beginning that need to be excluded
 parfiles = dir(fullfile(session, '*.par')); parfiles = {parfiles.name};
 niipaths = {}; parpaths = {}; num_runs = 0;
 while sum(contains(lower(niifiles), ['run' num2str(num_runs + 1) '.nii.gz'])) >= 1
@@ -40,6 +41,12 @@
     end
 end
 
+%Adding annotation for each run
+annotations = {};
+for i = 1:length(niipaths)
+    annotations{i} = ['localizer_run',num2str(i)];
+end
+
 % find path to anatomical inplane scan
 inplane_idx = find(contains(lower(niifiles), 'inplane'), 1);
 if isempty(inplane_idx)
@@ -81,7 +88,7 @@
 init_params.motionCompRefScan      = 1; % run number of reference scan for between-scans compensation
 
 % necessary fields that cannot be modified (maybe these can be hidden)
-init_params.sessionCode = session; % char array, session data directory
+init_params.sessionCode = session_id; % char array, local session data directory
 init_params.doAnalParams      = 1; % logical, set GLM analysis parameters during intialization
 init_params.doSkipFrames      = 1; % logical, clip countdown frames during initialization
 init_params.doPreprocessing   = 1; % logcial, do some preprocessing during initialization
@@ -92,10 +99,15 @@
 init_params.keepFrames = repmat([init_params.clip -1], num_runs, 1);
 
 % unnecessary fields that can be filled in by user
-init_params.subject     = ''; % char array with participant ID
-init_params.description = ''; % char array describing session
-init_params.comments    = ''; % char array of comments
-init_params.annotations = {}; % cell array of descriptions for each run
+init_params.subject     = session_id(1:find(session_id == '_') - 1); % char array with participant ID
+init_params.description = 'localizer'; % char array describing session
+init_params.comments    = 'Analyzed using fLoc'; % char array of comments
+init_params.annotations = annotations; % cell array of descriptions for each run
+
+%Alex noticed that the sessionDir needed to be changed so that the
+%mrSESSION.mat file would be added to the session's folder, not to the fLoc
+%folder
+init_params.sessionDir = session;
 
 
 %% Initialize and modify GLM analysis parameters
@@ -119,4 +131,6 @@
 glm_params.peakPeriod = 6:8;     % time window to estimate peak response
 glm_params.bslPeriod  = -4:0;    % time window to estiamte baseline response
 
+% annotation
+glm_params.annotation = sprintf('LocalizerGLM_%iruns',length(init_params.functionals));
 end