[ENH] compute tSNR for a given mask

demos/tSNR/tsnr_01_preproc.m

@@ -17,7 +17,7 @@
 bidsCopyInputFolder(opt);
 
 acq = {'2pt0', '2pt5', '3pt0'};
-for i = 1:numel(acq)
+for i = numel(acq)
   opt.query.acq = acq{i};
   bidsSpatialPrepro(opt);
 end

demos/tSNR/tsnr_03_compute.m

@@ -0,0 +1,43 @@
+% (C) Copyright 2019 Remi Gau
+
+clear;
+
+opt = tsnr_get_option();
+
+opt = checkOptions(opt);
+
+[BIDS, opt] = getData(opt, opt.dir.preproc);
+
+opt.dir.roi = fullfile(opt.dir.preproc, '..', 'cpp_spm-roi');
+opt = rmfield(opt, 'taskName');
+[BIDSroi, opt] = getData(opt, opt.dir.roi);
+
+% TODO ideally loop over subjects
+
+boldImage = bids.query(BIDS, 'data', 'sub', 'CTL05', 'suffix', 'bold', 'desc', 'preproc');
+referenceImg = bids.query(BIDS, 'data', 'sub', 'CTL05', 'suffix', 'bold', 'desc', 'mean');
+roi =  bids.query(BIDSroi, 'data', 'sub', 'CTL05');
+
+% TODO reslice for each acquisition resolution
+
+matlabbatch = {};
+matlabbatch = setBatchReslice(matlabbatch, opt, referenceImg, roi);
+spm_jobman('run', matlabbatch);
+
+opt.dir.preproc = opt.dir.roi;
+opt.query.modality = 'roi';
+opt = set_spm_2_bids_defaults(opt);
+name_spec.entities = struct('acq', 'xxx');
+opt.spm_2_bids = opt.spm_2_bids.add_mapping('prefix', 'r', ...
+                                            'name_spec', name_spec);
+opt.spm_2_bids = opt.spm_2_bids.flatten_mapping();
+
+bidsRename(opt);
+
+[tsnrImage, volTsnr] = computeTsnr(boldImage);
+
+[BIDSroi, opt] = getData(opt, opt.dir.roi);
+roi =  bids.query(BIDSroi, 'data', 'sub', 'CTL05', 'acq', 'xxx');
+
+% TODO loop over ROIs
+value = computeMeanValueInMask(tsnrImage, roi{1});

initCppSpm.m

@@ -1,51 +1,126 @@
 function initCppSpm()
-  %
-  % Adds the relevant folders to the path for a given session.
-  % Has to be run to be able to use CPP_SPM.
-  %
-  % USAGE::
-  %
-  %   initCppSpm()
-  %
-  % (C) Copyright 2021 CPP_SPM developers
-
-  opt.verbosity = 1;
-
-  global CPP_SPM_INITIALIZED
-
-  if isempty(CPP_SPM_INITIALIZED)
-
-    thisDirectory = fileparts(mfilename('fullpath'));
-
-    addpath(genpath(fullfile(thisDirectory, 'src')));
-    addpath(genpath(fullfile(thisDirectory, 'lib', 'spmup')));
-    addpath(genpath(fullfile(thisDirectory, 'lib', 'spm_2_bids')));
-
-    libList = { ...
-               'mancoreg', ...
-               'NiftiTools', ...
-               'bids-matlab', ...
-               'slice_display', ...
-               'panel-2.14', ...
-               'utils'};
-
-    for i = 1:numel(libList)
-      addpath(fullfile(thisDirectory, 'lib', libList{i}));
-    end
+    %
+    % Adds the relevant folders to the path for a given session.
+    % Has to be run to be able to use CPP_SPM.
+    %
+    % USAGE::
+    %
+    %   initCppSpm()
+    %
+    % (C) Copyright 2021 CPP_SPM developers
+
+    opt.verbosity = 1;
+
+    octaveVersion = '4.0.3';
+    matlabVersion = '8.6.0';
+
+    installlist = {'io', 'statistics', 'image'};
+
+    global CPP_SPM_INITIALIZED
+
+    if isempty(CPP_SPM_INITIALIZED)
+
+        thisDirectory = fileparts(mfilename('fullpath'));
+
+        addpath(genpath(fullfile(thisDirectory, 'src')));
+        addpath(genpath(fullfile(thisDirectory, 'lib', 'spmup')));
+        addpath(genpath(fullfile(thisDirectory, 'lib', 'spm_2_bids')));
+
+        libList = { ...
+            'mancoreg', ...
+            'NiftiTools', ...
+            'bids-matlab', ...
+            'slice_display', ...
+            'panel-2.14', ...
+            'utils'};
+
+        for i = 1:numel(libList)
+            addpath(fullfile(thisDirectory, 'lib', libList{i}));
+        end
+
+        addpath(fullfile(thisDirectory, 'lib', 'brain_colours', 'code'));
+        addpath(fullfile(thisDirectory, 'lib', 'riksneurotools', 'GLM'));
+
+        checkDependencies(opt);
+        printCredits(opt);
+
+        run(fullfile(thisDirectory, 'lib', 'CPP_ROI', 'initCppRoi'));
+
+        %%
+        if isOctave
+
+            % Exit if min version is not satisfied
+            if ~compare_versions(OCTAVE_VERSION, octaveVersion, '>=')
+                error('Minimum required Octave version: %s', octaveVersion);
+            end
 
-    addpath(fullfile(thisDirectory, 'lib', 'brain_colours', 'code'));
-    addpath(fullfile(thisDirectory, 'lib', 'riksneurotools', 'GLM'));
+            for ii = 1:length(installlist)
 
-    checkDependencies(opt);
-    printCredits(opt);
+                packageName = installlist{ii};
 
-    run(fullfile(thisDirectory, 'lib', 'CPP_ROI', 'initCppRoi'));
+                try
+                    % Try loading Octave packages
+                    disp(['loading ' packageName]);
+                    pkg('load', packageName);
 
-    CPP_SPM_INITIALIZED = true();
+                catch
 
-  else
-    printToScreen('\n\nCPP_SPM already initialized\n\n', opt);
+                    tryInstallFromForge(packageName);
 
-  end
+                end
+            end
+
+        else % MATLAB ----------------------------
+
+            if verLessThan('matlab', matlabVersion)
+                error('Sorry, minimum required MATLAB version is R2015b. :(');
+            end
+
+
+        end
+
+        CPP_SPM_INITIALIZED = true();
+
+    else
+        printToScreen('\n\nCPP_SPM already initialized\n\n', opt);
+
+    end
+
+    %   %-Detect SPM directory
+    % %--------------------------------------------------------------------------
+    % SPMdir = cellstr(which('spm.m','-ALL'));
+    % if isempty(SPMdir)
+    %     fprintf('SPM is not in your %s path.\n',software);
+    %     return;
+    % elseif numel(SPMdir) > 1
+    %     fprintf('SPM seems to appear in several different folders:\n');
+    %     for i=1:numel(SPMdir)
+    %         fprintf('  * %s\n',SPMdir{i});
+    %     end
+    %     fprintf('Remove all but one with ''pathtool'' or ''spm_rmpath''.\n');
+    %     return;
+    % else
+    %     fprintf('SPM is installed in: %s\n',fileparts(SPMdir{1}));
+    % end
+    % SPMdir = fileparts(SPMdir{1});
+
+end
+
+
+function tryInstallFromForge(packageName)
+
+    errorcount = 1;
+    while errorcount % Attempt twice in case installation fails
+        try
+            pkg('install', '-forge', packageName);
+            pkg('load', packageName);
+            errorcount = 0;
+        catch err
+            errorcount = errorcount + 1;
+            if errorcount > 2
+                error(err.message);
+            end
+        end
+    end
 
 end

miss_hit.cfg

@@ -23,6 +23,8 @@ copyright_entity: "Olivier Collignon"
 copyright_entity: "Mohamed Rezk"
 copyright_entity: "Remi Gau"
 copyright_entity: "CPP_SPM developers"
+copyright_entity: "Stephan Heunis"
+
 
 tab_width: 2
 

src/utils/computeMeanValueInMask.m

@@ -0,0 +1,22 @@
+function value = computeMeanValueInMask(image, mask)
+  %
+  % USAGE::
+  %
+  %   value = computeMeanValueInMask(image, mask)
+  %
+  % image: image filename
+  % mask: mask filename
+  %
+  %
+  % (C) Copyright 2021 CPP_SPM developers
+
+  % TODO what is returned by this when image is a 4D time series?
+  % write test
+
+  hdr = spm_vol(mask);
+  vol = spm_read_vols(hdr);
+  [x, y, z]  = ind2sub(size(vol), find(vol));
+  data     = spm_get_data(image, [x, y, z]');
+  value    = nanmean(data);
+
+end