add demo

Author: Remi-Gau

demos/roi/inputs/TStatistic.nii.gz

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+% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+
+%% examples to create ROIs and extract data
+%
+% ROI: use the probability map for visual motion from Neurosynth
+%   link: https://neurosynth.org/analyses/terms/visual%20motion/
+%
+% Data: tmap of Listening > Baseline from the MoAE demo
+
+clear;
+clc;
+
+%% ASSUMPTION
+%
+% This assumes that the 2 immages are in the same space (MNI, individual)
+% but they might not necessarily have the same resolution.
+%
+% In SPM lingo this means they are coregistered but not necessarily resliced.
+%
+
+%% IMPORTANT: for saving ROIs
+%
+% To save the ROIs, MarsBar must be installed: http://marsbar.sourceforge.net/
+%  - either in the "spm12/toolbox" folder
+%  - in the "cpp_spm/lib" folder
+%
+% https://sourceforge.net/projects/marsbar/files/marsbar/0.44/marsbar-0.44.zip/download
+%
+% cp -r /home/myhome/marsbar-0.44/* \
+%       /usr/local/spm/spm12/toolbox/marsbar
+%
+% If you want to save the ROI you are creating, you must make sure that the ROI
+% image you are using DOES have the same resolution as the image you will
+% sample.
+%
+% You can use the resliceRoiImages for that.
+
+%%
+probabilityMap = fullfile(pwd, 'inputs', 'visual motion_association-test_z_FDR_0.01.nii');
+dataImage = fullfile(pwd, 'inputs', 'TStatistic.nii');
+
+opt.unzip.do = true;
+opt.save.roi = true;
+if opt.save.roi
+  opt.reslice.do = true;
+else
+  opt.reslice.do = false;
+end
+
+[roiName, probabilityMap] = preprareDataAndROI(opt, dataImage, probabilityMap);
+data_mask = getDataFromMask(dataImage,  roiName);
+data_sphere = getDataFromSphere(opt, dataImage);
+data_intersection = getDataFromIntersection(opt, dataImage,  roiName);
+data_expand = getDataFromExpansion(opt, dataImage,  roiName);
+
+%% Mini functions
+
+% only to show how each case works
+
+function data_mask = getDataFromMask(dataImage, roiName)
+
+  data_mask = spm_summarise(dataImage, roiName);
+
+end
+
+function data_sphere = getDataFromSphere(opt, dataImage)
+
+  % X Y Z coordinates of right V5 in millimeters
+  location = [44 -67 0];
+
+  % radius in millimeters
+  radius = 5;
+
+  sphere.location = location;
+  sphere.radius = radius;
+
+  mask = createRoi('sphere', sphere, dataImage, opt.save.roi);
+
+  data_sphere = spm_summarise(dataImage, mask);
+
+  % equivalent to
+  % b = spm_summarise(dataImage, ...
+  %                   struct( ...
+  %                          'def', 'sphere', ...
+  %                          'spec', radius, ...
+  %                          'xyz', location'));
+
+end
+
+function data_intersection = getDataFromIntersection(opt, dataImage,  roiName)
+
+  % X Y Z coordinates of right V5 in millimeters
+  location = [44 -67 0];
+
+  sphere.location = location;
+  sphere.radius = 5;
+
+  mask = createRoi('intersection', roiName, sphere, dataImage, opt.save.roi);
+
+  data_intersection = spm_summarise(dataImage, mask.roi.XYZmm);
+
+end
+
+function data_expand = getDataFromExpansion(opt, dataImage,  roiName)
+
+  % X Y Z coordinates of right V5 in millimeters
+  location = [44 -67 0];
+
+  sphere.location = location;
+  sphere.radius = 1; % starting radius
+  sphere.maxNbVoxels = 50;
+
+  mask = createRoi('expand', roiName, sphere, dataImage, opt.save.roi);
+
+  data_expand = spm_summarise(dataImage, mask.roi.XYZmm);
+
+end
+
+%% HELPER FUNCTION
+
+function [roiName, probabilityMap] = preprareDataAndROI(opt, dataImage, probabilityMap)
+
+  if opt.unzip.do
+    gunzip(fullfile('inputs', '*.gz'));
+  end
+
+  if opt.reslice.do
+    % If needed reslice probability map to have same resolution as the data image
+    %
+    % resliceImg won't do anything if the 2 images have the same resolution
+    %
+    % if you read the data with spm_summarise,
+    % then the 2 images do not need the same resolution.
+    probabilityMap = resliceRoiImages(dataImage, probabilityMap);
+  end
+
+  % Threshold probability map into a binary mask
+  % to keep only values above a certain threshold
+  threshold = 10;
+  roiName = thresholdToMask(probabilityMap, threshold);
+
+end

demos/roi/inputs/sub-007_rSTSfmask_unc001.nii

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+mni_template = '/home/remi/matlab/SPM/spm12/canonical/avg152T1.nii';
+
+% X Y Z coordinates of right V5 in millimeters
+location = [44 -67 0];
+
+% radius in millimeters
+radius = 2;
+
+sphere.location = location;
+sphere.radius = radius;
+
+createRoi('sphere', sphere, mni_template, true);
+spm_smooth('sphere_2-44_-67_0.nii', 's2_sphere_2-44_-67_0.nii', [2 2 2], 4)