Humble attempt to fix typos by adding codespell action, config etc.

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,*.pdf,*.svg,*.js,_build,*.html,*.rtf,External
+# 
+ignore-words-list = ons,ans,fpr,ttests,myu,whos,ser,htmp,fwe,dout

.github/workflows/codespell.yml

@@ -0,0 +1,19 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v1

CanlabCore/@fmri_data/predict.m

@@ -108,7 +108,7 @@
 %        models), between eigenvectors, between scores, within 
 %        eigenvectors and within scores. Requires 'subjID' option followed 
 %        by size(obj.dat,2) x 1 vector of block labels.
-%        Optional: Concensus PCA, {'cpca', 1}. [Default]={'cpca, 0}.
+%        Optional: Consensus PCA, {'cpca', 1}. [Default]={'cpca, 0}.
 %        Optional: Dimension selection, {'numcomponents', [bt, wi]}.
 %                   [Default] = {'numcomponents',[Inf,Inf]} (df constrained)
 %        Note: You probably want to bootstrap this manually if
@@ -500,7 +500,7 @@
 %              -added nancorr to ignore nans when calculating correlation
 %              -added rng 'shuffle' to ensure that bootstrapping will use
 %              different inital seed.  VERY IMPORTANT for aggregating across
-%              multiple boostrap sessions!
+%              multiple bootstrap sessions!
 %
 %    11/28/13: Luke Chang
 %              -added ability to use hv block cross-validation, which is good

CanlabCore/@fmridisplay/addpoints.m

@@ -11,7 +11,7 @@
 % - enter xyz as n x 3 list of coordinates in mm to plot (world space)
 % - Points or text labels or both
 % - Flexible slice spacing, colors, marker sizes/styles, axis layout (one row/standard square)
-% - axial, saggital, or coronal orientation handled automatically
+% - axial, sagittal, or coronal orientation handled automatically
 % - Multiple different sets of points can be plotted in different colors/text labels
 %
 % :Optional Inputs:
@@ -178,7 +178,7 @@
             case 'axial'
                 whcol = 3;
 
-            case {'sagg', 'sagittal', 'saggital'}
+            case {'sagg', 'sagittal', 'sagittal'}
 
                 whcol = 1;
 

CanlabCore/@fmridisplay/fmridisplay.m

@@ -27,17 +27,17 @@
 % obj = montage(obj, 'spacing', 4);
 % obj = addblobs(obj, cl, 'trans', 'color', [0 0 1], 'smooth');
 %
-% Add axial and parasaggital montages to the same figure:
+% Add axial and parasagittal montages to the same figure:
 % o2 = montage(o2, 'axial', 'slice_range', [-40 50], 'onerow', 'spacing', 6);
 % axh = axes('Position', [0.03 0.45 .1 .5]);
-% o2 = montage(o2, 'saggital', 'wh_slice', [0 0 0], 'existing_axes', axh);
+% o2 = montage(o2, 'sagittal', 'wh_slice', [0 0 0], 'existing_axes', axh);
 %
 % Add blue outlines only:
 % obj = addblobs(obj, cl, 'outline', 'color', [0 0 1]);
 %
 % Sagittal images and blobs:
 % o2 = fmridisplay;
-% o2 = montage(o2, 'saggital', 'slice_range', [-20 20], 'onerow');
+% o2 = montage(o2, 'sagittal', 'slice_range', [-20 20], 'onerow');
 % o2 = addblobs(o2, cl);
 % legend(o2, 'figure')
 % o2 = addblobs(o2, cl, 'contour', 'color', [0 1 0]);
@@ -48,7 +48,7 @@
 %
 % Overlapping sagittal and axial images with outlines
 % o2 = fmridisplay;
-% o2 = montage(o2, 'saggital', 'slice_range', [-10 10], 'onerow');
+% o2 = montage(o2, 'sagittal', 'slice_range', [-10 10], 'onerow');
 % enlarge_axes(gcf, 1.2);
 % o2 = montage(o2, 'axial', 'slice_range', [-40 50], 'onerow', 'spacing', 4);
 % o2 = addblobs(o2, cl, 'splitcolor', {[0 0 1] [.3 0 .8] [.8 .3 0] [1 1 0]});
@@ -59,7 +59,7 @@
 % o2 = addblobs(o2, cl, 'splitcolor', {[0 0 1] [0 1 1] [1 .5 0] [1 1 0]}, 'cmaprange', [-2 2], 'trans');
 % o2 = addblobs(o2, cl, 'splitcolor', {[0 0 1] [0 1 1] [1 .5 0] [1 1 0]}, 'cmaprange', [-2 2], 'transvalue', .85);
 %
-% o2 = montage(o2, 'saggital', 'slice_range', [-6 6], 'onerow');
+% o2 = montage(o2, 'sagittal', 'slice_range', [-6 6], 'onerow');
 % o2 = montage(o2, 'axial', 'slice_range', [-20 30], 'onerow', 'spacing', 8);
 % xyz = a list of [x y z] coordinates, one coord per row
 % o2 = montage(o2, 'axial', 'wh_slice', xyz, 'onerow');

CanlabCore/@fmridisplay/montage.m

@@ -3,7 +3,7 @@
 %  - Solid brain slices or contour outlines
 %  - Points or text labels or both
 %  - Flexible slice spacing, colors, marker sizes/styles, axis layout (one row/standard square)
-%  - axial or saggital orientation
+%  - axial or sagittal orientation
 %
 % :Usage:
 % ::
@@ -36,7 +36,7 @@
 %   **{'close', 'closeenough', 'close_enough'}:**
 %        close_enough =    varargin{i+1};
 %
-%   **{'sagg','saggital','sagittal'}:**
+%   **{'sagg','sagittal','sagittal'}:**
 %        orientation = 'sagittal';
 %
 %   **{'MarkerSize', 'markersize'}:**
@@ -70,7 +70,7 @@
 %        followed my mm values for slices desired
 %      e.g., for cluster/region centers, xyz = cat(1, cl.mm_center)
 %      o2 = montage(o2, 'axial', 'wh_slice', xyz, 'onerow');
-%      o2 = montage(o2, 'saggital', 'wh_slice', xyz, 'onerow');
+%      o2 = montage(o2, 'sagittal', 'wh_slice', xyz, 'onerow');
 %
 %   **'spacing':**
 %        followed by inter-slice spacing in mm
@@ -109,15 +109,15 @@
 % ::
 %
 %    axh = axes('Position', [0.05 0.4 .1 .5]);
-%    o2 = montage(o2, 'saggital', 'wh_slice', xyz(1,:), 'existing_axes', axh);
+%    o2 = montage(o2, 'sagittal', 'wh_slice', xyz(1,:), 'existing_axes', axh);
 %
-%    o2 = montage(o2, 'saggital', 'slice_range', [-10 10], 'onerow');
+%    o2 = montage(o2, 'sagittal', 'slice_range', [-10 10], 'onerow');
 %    o2 = montage(o2, 'axial', 'slice_range', [-40 50], 'onerow', 'spacing', 4);
 %    o2 = montage(o2, 'axial', 'slice_range', [-20 30], 'onerow', 'spacing', 8);
 %    o2 = montage(o2, 'axial', 'wh_slice', xyz, 'onerow');
 %
-%    % Parasaggital only:
-%    o2 = montage(o2, 'saggital', 'slice_range', [-4 4], 'onerow', 'spacing', 8);
+%    % Parasagittal only:
+%    o2 = montage(o2, 'sagittal', 'slice_range', [-4 4], 'onerow', 'spacing', 8);
 %
 % Add/remove blobs and points with fmridisplay.addblobs,
 % fmridisplay.addpoints, fmridisplay.removeblobs, fmridisplay.removepoints
@@ -194,7 +194,7 @@
                 varargin{i+1} = [];
                 varargin{i} = [];
 
-            case {'sag', 'sagg','saggital','sagittal'}, myview = 'sagittal';
+            case {'sag', 'sagg','sagittal','sagittal'}, myview = 'sagittal';
 
             case {'cor', 'coronal'}, myview = 'coronal';
 

CanlabCore/@fmridisplay/zoom_in_on_regions.m

@@ -2,7 +2,7 @@ function zoom_in_on_regions(o2, cl, orientation)
 % Assumes you have one axis per region in a montage registered in an
 % fmridisplay object (o2). Given the object o2, which montage to adjust
 % (montage_num), a corresponding region object with coordinates (cl), and an
-% orientation ('axial', 'saggital', or 'coronal'), this object method zooms 
+% orientation ('axial', 'sagittal', or 'coronal'), this object method zooms 
 % in on each cluster by adjusting the axes.  
 %
 % Tor Wager, Feb 2018
@@ -25,7 +25,7 @@ function zoom_in_on_regions(o2, cl, orientation)
             xl = xyzminmax(1, :);
             yl = xyzminmax(2, :);
 
-        case 'saggital'
+        case 'sagittal'
             xl = xyzminmax(2, :);
             yl = xyzminmax(3, :);
 

CanlabCore/@image_vector/display_slices.m

@@ -1,7 +1,7 @@
 function [whsl, plate] = display_slices(dat, varargin)
 % Creates 3 separate montage views - ax, cor, sagg in a special figure window
 %
-% - By default, a figure with axial, coronal, and saggital montages are
+% - By default, a figure with axial, coronal, and sagittal montages are
 % created.  But it's also easy to create nicer-looking separate figures with
 % only one view.
 % - Also easy to select slices: Enter 'startslice' and 'endslice', each followed by values, to display
@@ -20,7 +20,7 @@
 %
 % :Inputs:
 %
-% **'axial', 'saggital', 'sagittal', 'coronal':**
+% **'axial', 'sagittal', 'sagittal', 'coronal':**
 %   Keywords to control view
 % 
 % **'spacing'**
@@ -60,14 +60,14 @@
 %
 %     display_slices(dat);
 %     display_slices(dat, 'coronal');
-%     display_slices(dat, 'saggital', 'spacing', 10); % 10 mm spacing
-%     display_slices(dat, 'saggital', 'spacing', 10, 'vertical');
-%     display_slices(dat, 'saggital', 'slices_per_row', 12);
+%     display_slices(dat, 'sagittal', 'spacing', 10); % 10 mm spacing
+%     display_slices(dat, 'sagittal', 'spacing', 10, 'vertical');
+%     display_slices(dat, 'sagittal', 'slices_per_row', 12);
 %     display_slices(dat, 'axial', 'slices_per_row', 20, 'spacing', 4, 'startslice', -10, 'endslice', 10); % z = -10 to 10 mm, 4 mm spacing
 %
 % Make a montage of a subset of slices and make it fill the figure:
 % create_figure('sagg')
-% display_slices(dat, 'saggital', 'slices_per_row', 4, 'spacing', 3, 'startslice', -20, 'endslice', 20)
+% display_slices(dat, 'sagittal', 'slices_per_row', 4, 'spacing', 3, 'startslice', -20, 'endslice', 20)
 % set(gca, 'Position', [.05 .05 .9 1]);
 % colormap gray
 %
@@ -96,7 +96,7 @@
     if ischar(varargin{i})
         switch varargin{i}
             % reserved keywords
-            case {'axial', 'saggital', 'sagittal', 'coronal'}, myview = varargin{i};
+            case {'axial', 'sagittal', 'sagittal', 'coronal'}, myview = varargin{i};
             case 'spacing', spacing = varargin{i + 1};
             case 'vertical', stackorient = 1;
             case 'slices_per_row', s = varargin{i + 1};
@@ -127,7 +127,7 @@
     fh = create_figure('slice_display');
     axis off
     ax1 = axes('OuterPosition', [.05 .05 .20 .90], 'Position', [.05 .05 .20 .90]);
-    display_slices(dat, 'saggital', 'spacing', 8, 'vertical');
+    display_slices(dat, 'sagittal', 'spacing', 8, 'vertical');
 
     ax2 = axes('OuterPosition', [.229 .05 .8 .150]); %[.20 .05 .8 .30]);
     set(ax2, 'Position', get(ax2, 'OuterPosition'));
@@ -160,7 +160,7 @@
 switch myview
     case 'axial'
         wh_col = 3;
-    case {'saggital', 'sagittal'}
+    case {'sagittal', 'sagittal'}
         wh_col = 1;
     case 'coronal'
         wh_col = 2;
@@ -240,7 +240,7 @@ otherwise error('unknown slice view.')
            subvol = abs(vdat(:, :, whsl));
            sumabsval = sum(sum(subvol, 1), 2);
 
-       case {'saggital', 'sagittal'}
+       case {'sagittal', 'sagittal'}
            subvol = abs(vdat(whsl, :, :));
            sumabsval = sum(sum(subvol, 2), 3);
 
@@ -285,7 +285,7 @@ otherwise error('unknown slice view.')
             case 'axial'
                 stacked{i} = vdat(:, :, i);
                 stacked{i} = rot90(stacked{i});
-            case {'saggital', 'sagittal'}
+            case {'sagittal', 'sagittal'}
                 stacked{i} = squeeze(vdat(i, :, :));
                 stacked{i} = rot90(stacked{i});
             case 'coronal'
@@ -361,7 +361,7 @@ otherwise error('unknown slice view.')
     nullvox = vdat == 0 | isnan(vdat);
     bottom = all(nullvox, 3);
 
-    if strcmp(myview, 'saggital') || strcmp(myview, 'sagittal')
+    if strcmp(myview, 'sagittal') || strcmp(myview, 'sagittal')
         % skip
     else
         nullx = squeeze(all(bottom, 2));

CanlabCore/@image_vector/slices.m

@@ -13,7 +13,7 @@
 % :Optional Inputs:
 %
 %   **orientation:**
-%        can be followed by 'saggital', 'axial', or 'coronal'
+%        can be followed by 'sagittal', 'axial', or 'coronal'
 %
 %   **slice_mm:**
 %        is followed by the mm coord of the slice to display; default = 0
@@ -50,14 +50,14 @@
 %    slices(dat, 'slice', -5);                 % display sagg at x = -5
 %    o = slices(dat, 'names', terms); % use 'terms' var as names
 %
-%    o2 = slices(all_chi2_images, 'orientation', 'saggital', 'slice', 0);
+%    o2 = slices(all_chi2_images, 'orientation', 'sagittal', 'slice', 0);
 %
 % ..
 %    Copyright 2011, Tor Wager
 % ..
 
 slice_mm = 0;
-my_orientation = 'saggital';
+my_orientation = 'sagittal';
 nimgs = size(obj.dat, 2);
 dosplitcolor = 1;
 outlinecolor = [];

CanlabCore/@statistic_image/multi_threshold.m

@@ -369,7 +369,7 @@
 %             
             %             o2 = montage(o2, 'axial', 'slice_range', [-40 50], 'onerow', 'spacing', 6, 'noverbose');
             %             axh = axes('Position', [0.05 0.4 .1 .5]);
-            %             o2 = montage(o2, 'saggital', 'wh_slice', [0 0 0], 'existing_axes', axh, 'noverbose');
+            %             o2 = montage(o2, 'sagittal', 'wh_slice', [0 0 0], 'existing_axes', axh, 'noverbose');
 
         end
     end

CanlabCore/Cluster_contig_region_tools/Cluster-based_multivar_tools/cluster_nmdsfig.m

@@ -288,8 +288,8 @@
     %     cluster_orthviews_showcenters(cl,'coronal',overlay);
     %     save_figure('cluster_slices_coronal');
     %
-    %     cluster_orthviews_showcenters(cl,'saggital',overlay);
-    %     save_figure('cluster_slices_saggital');
+    %     cluster_orthviews_showcenters(cl,'sagittal',overlay);
+    %     save_figure('cluster_slices_sagittal');
 end
 
 diary off

CanlabCore/Data_extraction/readim2.m

@@ -14,7 +14,7 @@
 %        to plot montage of slices to the screen
 %
 %   **sagg:**
-%        to rotate to saggital view
+%        to rotate to sagittal view
 %
 %   **cor:**
 %        to rotate to coronal view

CanlabCore/ROI_drawing_tools/draw_anatomical_roi.m

@@ -45,8 +45,8 @@
 vol = double(vol);
 
 
-dosagg = input('Press 1 to choose saggital slices, or 0 for axial.');
-% if saggital, use vol, not rvol
+dosagg = input('Press 1 to choose sagittal slices, or 0 for axial.');
+% if sagittal, use vol, not rvol
 % y is not reversed
 % ginput x = brain y, ginput y = brainz, slice = x
 

CanlabCore/ROI_drawing_tools/draw_anatomical_roi_2008.m

@@ -107,7 +107,7 @@ function draw_anatomical_roi_2008(meth, varargin)
             meth = 'exit';
 
         case 'freesagg'
-            disp('Draw freehand region on the saggital slice in Slices fig.');
+            disp('Draw freehand region on the sagittal slice in Slices fig.');
             data = get_gui_data;
             axis_handle = data.saggh;
             draw_freehand(axis_handle);
@@ -667,7 +667,7 @@ function smooth_vol(varargin)
 str = 'draw_anatomical_roi_2008(''freesagg'');';
 str = expand_callback_str(str);
 
-uicontrol(f,'String','Draw (saggital)',...
+uicontrol(f,'String','Draw (sagittal)',...
 'Position',[x2start 200-35*0 150 30],...
 'CallBack', str,...
 'Interruptible','on',...

CanlabCore/Statistics_tools/Cross_validated_Regression/xval_bestsubsets_brain.m

@@ -537,7 +537,7 @@
 % % % CV(1) (leave-one-out cross-validation)
 % % % it estimates "half-sample" xval
 % %
-% % bootfun = @(Y, X) xval_regression_boostrap_wrapper(Y, X);
+% % bootfun = @(Y, X) xval_regression_bootstrap_wrapper(Y, X);
 % % STATS_FINAL.bootstrap.covs_only_r_rsq = bootstrp(200, bootfun, my_outcomes_orig{1}, covs{1});
 % % STATS_FINAL.bootstrap.covs_only_summary = [mean(STATS_FINAL.bootstrap.covs_only_r_rsq) std(STATS_FINAL.bootstrap.covs_only_r_rsq) ];
 % % STATS_FINAL.bootstrap.covs_only_summary_descrip = 'mean std of bootstrapped values'

CanlabCore/Statistics_tools/Cross_validated_Regression/xval_lasso_brain.m

@@ -618,7 +618,7 @@
 % % % CV(1) (leave-one-out cross-validation)
 % % % it estimates "half-sample" xval
 % %
-% % bootfun = @(Y, X) xval_regression_boostrap_wrapper(Y, X);
+% % bootfun = @(Y, X) xval_regression_bootstrap_wrapper(Y, X);
 % % STATS_FINAL.bootstrap.covs_only_r_rsq = bootstrp(200, bootfun, my_outcomes_orig{1}, covs{1});
 % % STATS_FINAL.bootstrap.covs_only_summary = [mean(STATS_FINAL.bootstrap.covs_only_r_rsq) std(STATS_FINAL.bootstrap.covs_only_r_rsq) ];
 % % STATS_FINAL.bootstrap.covs_only_summary_descrip = 'mean std of bootstrapped values'

CanlabCore/Statistics_tools/Cross_validated_Regression/xval_lasso_brain_featureselect.m

@@ -455,7 +455,7 @@ function permuted_histogram_plot(STATS_FINAL)
 % % % CV(1) (leave-one-out cross-validation)
 % % % it estimates "half-sample" xval
 % %
-% % bootfun = @(Y, X) xval_regression_boostrap_wrapper(Y, X);
+% % bootfun = @(Y, X) xval_regression_bootstrap_wrapper(Y, X);
 % % STATS_FINAL.bootstrap.covs_only_r_rsq = bootstrp(200, bootfun, my_outcomes_orig{1}, covs{1});
 % % STATS_FINAL.bootstrap.covs_only_summary = [mean(STATS_FINAL.bootstrap.covs_only_r_rsq) std(STATS_FINAL.bootstrap.covs_only_r_rsq) ];
 % % STATS_FINAL.bootstrap.covs_only_summary_descrip = 'mean std of bootstrapped values'

CanlabCore/Statistics_tools/Cross_validated_Regression/xval_regression_multisubject_bootstrapweightmap.m

@@ -547,7 +547,7 @@ function nested_choose_ndims()
         obj = montage(obj, 'onerow');  % Show axial montage of underlay
         %obj = montage(obj, 'axial', 'slice_range', [-40 55], 'onerow', 'spacing', 8);
         enlarge_axes(gcf, .95);
-        obj = montage(obj, 'saggital', 'slice_range', [-6 6], 'onerow');
+        obj = montage(obj, 'sagittal', 'slice_range', [-6 6], 'onerow');
 
         for i = 1:length(thresh)
 

CanlabCore/Statistics_tools/Cross_validated_Regression/xval_ridge_brain.m

@@ -494,7 +494,7 @@
 % % % CV(1) (leave-one-out cross-validation)
 % % % it estimates "half-sample" xval
 % %
-% % bootfun = @(Y, X) xval_regression_boostrap_wrapper(Y, X);
+% % bootfun = @(Y, X) xval_regression_bootstrap_wrapper(Y, X);
 % % STATS_FINAL.bootstrap.covs_only_r_rsq = bootstrp(200, bootfun, my_outcomes_orig{1}, covs{1});
 % % STATS_FINAL.bootstrap.covs_only_summary = [mean(STATS_FINAL.bootstrap.covs_only_r_rsq) std(STATS_FINAL.bootstrap.covs_only_r_rsq) ];
 % % STATS_FINAL.bootstrap.covs_only_summary_descrip = 'mean std of bootstrapped values'