ref

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 7
+metric "cnest": limit 4
 metric "file_length": limit 1000
-metric "cyc": limit 22
-metric "parameters": limit 9
+metric "cyc": limit 20
+metric "parameters": limit 6

createMontage.m → src/plotting/createMontage.m

@@ -11,12 +11,14 @@
   %                         'cxs', [0 255])
   %
   %
-  % Simple function to create a montage / mosaic of multiple slices from a single 3D
+  % 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)
+  % 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?
@@ -116,27 +118,7 @@
     montage.whole_img = whole;
   end
 
-  % Get screen size for plotting - [1 1 w h]
-  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
+  f = initMontageFigure(shape, visibility);
 
   ax = subplot(1, 1, 1);
   im = imagesc(ax, montage.whole_img);

createOverlayMontage.m → src/plotting/createOverlayMontage.m

@@ -1,6 +1,6 @@
 function output = createOverlayMontage(varargin)
 
-  % (C) Copyright 2022 bidspm developers
+  % (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});
@@ -55,9 +55,7 @@
                                    'cxs', cxs);
 
   % Create figures with background montage and overlaid masks
-  f = figure('units', 'normalized', ...
-             'outerposition', [0 0 1 1], ...
-             'visible', visibility);
+  f = initMontageFigure(shape, visibility);
   imagesc(montage_template.whole_img);
   colormap(cmap);
   if ~isempty(cxs)
@@ -77,7 +75,8 @@
 
   if iscell(overlayImg)
     for i = 1:numel(overlayImg)
-      montage_overlay{i} = createMontage(overlayImg{i},   'columns', columns, ...
+      montage_overlay{i} = createMontage(overlayImg{i}, ...
+                                         'columns', columns, ...
                                          'rotate', rotate, ...
                                          'cmap', cmap, ...
                                          'visibility', 'off', ...
@@ -86,7 +85,8 @@
     end
   else
     montage_overlay = {};
-    montage_overlay{1} = createMontage(overlayImg,   'columns', columns, ...
+    montage_overlay{1} = createMontage(overlayImg, ...
+                                       'columns', columns, ...
                                        'rotate', rotate, ...
                                        'cmap', cmap, ...
                                        'visibility', 'off', ...
@@ -103,7 +103,8 @@
       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);
+        p = plot(ax, bound_whole_bin{b, 1}(:, 2), bound_whole_bin{b, 1}(:, 1), ...
+                 'color', rbgclr, 'LineWidth', 1);
       end
     end
   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

@@ -3,9 +3,15 @@
 
 bidspm_dir = '/home/remi/github/cpp-lln-lab/bidspm';
 
-overlay_img = fullfile(bidspm_dir, 'demos/MoAE/outputs/derivatives/bidspm-stats/sub-01/task-auditory_space-MNI152NLin6Asym_FWHM-8/mask.nii');
+demos_dir = fullfile(bidspm_dir, 'demos/MoAE/outputs/derivatives/');
 
-template_img = fullfile(bidspm_dir, 'demos/MoAE/outputs/derivatives/bidspm-preproc/sub-01/func/sub-01_task-auditory_space-MNI152NLin6Asym_desc-smth8_bold.nii');
+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));
@@ -14,4 +20,5 @@
 mask = spm_read_vols(mask_hdr);
 
 % createMontage(template, 'shape', 'square');
-createOverlayMontage(template, mask, 'rgbcolors', [255, 0, 0], 'shape', 'square');
+createOverlayMontage(template, mask, 'rgbcolors', [255, 0, 0], ...
+                     'shape', 'square');