plot figure mask glm

miss_hit.cfg

@@ -36,7 +36,7 @@ copyright_entity: "Wellcome Trust Centre for Neuroimaging"
 tab_width: 2
 
 # metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
-metric "cnest": limit 5
+metric "cnest": limit 4
 metric "file_length": limit 1000
-metric "cyc": limit 22
-metric "parameters": limit 7
+metric "cyc": limit 20
+metric "parameters": limit 6

src/plotting/createMontage.m

@@ -0,0 +1,135 @@
+function montage = createMontage(varargin)
+  %
+  % USAGE
+  %
+  % montage = createMontage(img, ...
+  %                         'columns', 9, ...
+  %                         'rotate', true, ...
+  %                         'cmap', 'gray', ...
+  %                         'visibility', 'on', ...
+  %                         'shape', 'max', ...
+  %                         'cxs', [0 255])
+  %
+  %
+  % Simple function to create a montage /
+  %  mosaic of multiple slices from a single 3D
+  % image matrix.
+  %
+  % INPUT:
+  % img           - 3D (x,y,z) image matrix
+  % columns       - number of columns in montage
+  % (rows are calculated accordingly)
+  % rotate        - rotate images 90 deg clockwise? yes = 1; no = 0.
+  % cmap          - figure colormap
+  % visibility    - show figure?
+  %
+  % OUTPUT:
+  % output        - structure with montage data
+
+  % (C) Copyright 2022 bidspm developers
+
+  % TODO: Needs improvement i.t.o RAS/LAS orientation specification
+  %  and image layout...
+
+  args = inputParser;
+
+  addRequired(args, 'img');
+  addParameter(args, 'columns', 9, @isnumeric);
+  addParameter(args, 'rotate', true, @islogical);
+  addParameter(args, 'cmap', 'gray', @ischar);
+  addParameter(args, 'visibility', 'on', @ischar);
+  addParameter(args, 'shape', 'max', @ischar); % max or square
+  addParameter(args, 'cxs', 'auto');
+
+  parse(args, varargin{:});
+
+  img = args.Results.img;
+  columns = args.Results.columns;
+  rotate = args.Results.rotate;
+  cmap = args.Results.cmap;
+  visibility = args.Results.visibility;
+  shape = args.Results.shape;
+  cxs = args.Results.cxs;
+
+  montage = struct;
+  [Ni, Nj, Nk] = size(img);
+
+  % Rotate image slices if required
+  if rotate
+    img_orig = img;
+    clear img;
+    for p = 1:Nk
+      img(:, :, p) = rot90(img_orig(:, :, p));
+    end
+  end
+
+  % Determine amount of rows and filler slices
+  rows = floor(Nk / columns);
+  if rows == 0
+    rows = 1;
+  end
+  fill = mod(Nk, columns);
+  if fill == 0
+    N_fill = 0;
+  else
+    N_fill = columns - mod(Nk, columns);
+  end
+  if rotate
+    filler = zeros(Nj, Ni);
+  else
+    filler = zeros(Ni, Nj);
+  end
+
+  montage.rows = rows;
+  montage.columns = columns;
+  montage.N_fill = N_fill;
+
+  parts = {};
+  % 1 - Concatenate slices together horizontally, per row (except last).
+  % 2 - Concatenate rows together vertically
+  for i = 1:rows
+    for j = 1:columns
+      if j == 1
+        parts{i} = img(:, :, columns * (i - 1) + j);
+      else
+        parts{i} = cat(2, parts{i}, img(:, :, columns * (i - 1) + j));
+      end
+    end
+    if i == 1
+      whole = parts{i};
+    else
+      whole = cat(1, whole, parts{i});
+    end
+  end
+
+  % 1 - Concatenate filler slices to last row, if required.
+  % 2 - Concatenate last row to whole matrix, if required.
+  if N_fill ~= 0
+    % last row
+    last_parts = img(:, :, rows * columns + 1);
+    for k = (rows * columns + 2):Nk
+      last_parts = cat(2, last_parts, img(:, :, k));
+    end
+    for m = 1:N_fill
+      last_parts = cat(2, last_parts, filler);
+    end
+    montage.whole_img = cat(1, whole, last_parts);
+  else
+    montage.whole_img = whole;
+  end
+
+  f = initMontageFigure(shape, visibility);
+
+  ax = subplot(1, 1, 1);
+  im = imagesc(ax, montage.whole_img);
+
+  colormap(cmap);
+  if ~isempty(cxs)
+    caxis(ax, cxs);
+  end
+
+  montage.im = im;
+  montage.f = f;
+  montage.ax = ax;
+
+end

src/plotting/createOverlayMontage.m

@@ -0,0 +1,133 @@
+function output = createOverlayMontage(varargin)
+
+  % (C) Copyright 2024 bidspm developers
+
+  % fmrwhy_util_createOverlayMontage(tsnr_img{i}, overlayImg, 9, 1, '', ...
+  % 'hot', 'off', 'max', [0 250], [33, 168, 10], tsnr_saveAss{i});
+
+  % Function to create montages of images/rois overlaid on a template image
+
+  rgbcolors = [255, 255, 191; ...
+               215, 25, 28; ...
+               253, 174, 97; ...
+               171, 217, 233; ...
+               44, 123, 182];
+
+  args = inputParser;
+
+  addRequired(args, 'templateImg');
+  addRequired(args, 'overlayImg');
+  addParameter(args, 'columns', 9, @isnumeric);
+  addParameter(args, 'rotate', true, @islogical);
+  addParameter(args, 'cmap', 'gray', @ischar);
+  addParameter(args, 'visibility', 'on', @ischar);
+  addParameter(args, 'shape', 'max', @ischar); % max or square
+  addParameter(args, 'cxs', 'auto');
+  addParameter(args, 'rgbcolors', rgbcolors);
+  addParameter(args, 'saveAs', '');
+
+  parse(args, varargin{:});
+
+  templateImg = args.Results.templateImg;
+  overlayImg = args.Results.overlayImg;
+  columns = args.Results.columns;
+  rotate = args.Results.rotate;
+  cmap = args.Results.cmap;
+  visibility = args.Results.visibility;
+  shape = args.Results.shape;
+  cxs = args.Results.cxs;
+  rgbcolors = args.Results.rgbcolors;
+  saveAs = args.Results.saveAs;
+
+  % Structure to save output
+  output = struct;
+  alpha = 0.2;
+  plot_contour = 1;
+  rgbcolors = rgbcolors / 255;
+
+  % Create background montage
+  montage_template = createMontage(templateImg, ...
+                                   'columns', columns, ...
+                                   'rotate', rotate, ...
+                                   'cmap', cmap, ...
+                                   'visibility', 'off', ...
+                                   'shape', shape, ...
+                                   'cxs', cxs);
+
+  % Create figures with background montage and overlaid masks
+  f = initMontageFigure(shape, visibility);
+  imagesc(montage_template.whole_img);
+  colormap(cmap);
+  if ~isempty(cxs)
+    caxis(cxs);
+  end
+  ax = gca;
+  outerpos = ax.OuterPosition;
+  ti = ax.TightInset;
+  left = outerpos(1) + ti(1);
+  bottom = outerpos(2) + ti(2);
+  ax_width = outerpos(3) - ti(1) - ti(3);
+  ax_height = outerpos(4) - ti(2) - ti(4);
+  ax.Position = [left bottom ax_width ax_height];
+  hold(ax, 'on');
+  [Nimx, Nimy] = size(montage_template.whole_img);
+  oo = ones(Nimx, Nimy);
+
+  if iscell(overlayImg)
+    for i = 1:numel(overlayImg)
+      montage_overlay{i} = createMontage(overlayImg{i}, ...
+                                         'columns', columns, ...
+                                         'rotate', rotate, ...
+                                         'cmap', cmap, ...
+                                         'visibility', 'off', ...
+                                         'shape', shape, ...
+                                         'cxs', 'auto');
+    end
+  else
+    montage_overlay = {};
+    montage_overlay{1} = createMontage(overlayImg, ...
+                                       'columns', columns, ...
+                                       'rotate', rotate, ...
+                                       'cmap', cmap, ...
+                                       'visibility', 'off', ...
+                                       'shape', shape, ...
+                                       'cxs', 'auto');
+  end
+
+  for i = 1:numel(montage_overlay)
+    rbgclr = rgbcolors(i, :);
+    clr = cat(3, rbgclr(1) * oo, rbgclr(2) * oo, rbgclr(3) * oo);
+    imC = imagesc(ax, clr);
+    set(imC, 'AlphaData', alpha * montage_overlay{i}.whole_img);
+    if plot_contour
+      bound_whole_bin = bwboundaries(montage_overlay{i}.whole_img);
+      Nblobs_bin = numel(bound_whole_bin);
+      for b = 1:Nblobs_bin
+        p = plot(ax, bound_whole_bin{b, 1}(:, 2), bound_whole_bin{b, 1}(:, 1), ...
+                 'color', rbgclr, 'LineWidth', 1);
+      end
+    end
+  end
+
+  hold(ax, 'off');
+  set(ax, 'xtick', []);
+  set(ax, 'xticklabel', []);
+  set(ax, 'ytick', []);
+  set(ax, 'yticklabel', []);
+  set(ax, 'ztick', []);
+  set(ax, 'zticklabel', []);
+
+  output.ax = ax;
+  output.f = f;
+
+  if saveAs ~= 0
+    print(f, saveAs, '-dpng', '-r0');
+  end
+  % Close necessary figure handles
+  close(montage_template.f);
+  for i = 1:numel(montage_overlay)
+    close(montage_overlay{i}.f);
+  end
+  if strcmp(visibility, 'off')
+    close(f);
+  end

src/plotting/initMontageFigure.m

@@ -0,0 +1,24 @@
+function f = initMontageFigure(shape, visibility)
+  % (C) Copyright 2024 bidspm developers
+
+  scr_size = get(0, 'ScreenSize');
+  dist = scr_size(4);
+  if scr_size(3) < dist
+    dist = scr_size(3);
+  end
+  % Create figure - outerposition = [left bottom width height]
+
+  if strcmp(shape, 'max')
+    f = figure('visible', visibility, ...
+               'units', 'normalized', ...
+               'outerposition', [0 0 1 1]);
+  elseif strcmp(shape, 'square')
+    f = figure('visible', visibility, ...
+               'units', 'pixels', ...
+               'outerposition', [0 0 dist dist]);
+  else
+    f = figure('visible', visibility, ...
+               'units', 'pixels', ...
+               'outerposition', [0 0 dist dist]);
+  end
+end

untitled.m

@@ -0,0 +1,24 @@
+% (C) Copyright 2022 bidspm developers
+close all;
+
+bidspm_dir = '/home/remi/github/cpp-lln-lab/bidspm';
+
+demos_dir = fullfile(bidspm_dir, 'demos/MoAE/outputs/derivatives/');
+
+overlay_img = fullfile(demos_dir, ...
+                       'bidspm-stats/sub-01/task-auditory_space-MNI152NLin6Asym_FWHM-8/mask.nii');
+
+template_img = fullfile( ...
+                        demos_dir, ...
+                        'bidspm-preproc', 'sub-01', 'func', ...
+                        'sub-01_task-auditory_space-MNI152NLin6Asym_desc-smth8_bold.nii');
+
+template_hdr = spm_vol(template_img);
+template = spm_read_vols(template_hdr(1));
+
+mask_hdr = spm_vol(overlay_img);
+mask = spm_read_vols(mask_hdr);
+
+% createMontage(template, 'shape', 'square');
+createOverlayMontage(template, mask, 'rgbcolors', [255, 0, 0], ...
+                     'shape', 'square');