diff --git a/.codespellrc b/.codespellrc
new file mode 100644
index 00000000..f3359c32
--- /dev/null
+++ b/.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
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
new file mode 100644
index 00000000..5768d7c6
--- /dev/null
+++ b/.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
diff --git a/CanlabCore/@fmri_data/predict.m b/CanlabCore/@fmri_data/predict.m
index 6e78c0c0..2dae2be1 100644
--- a/CanlabCore/@fmri_data/predict.m
+++ b/CanlabCore/@fmri_data/predict.m
@@ -107,8 +107,8 @@
% total model, between model, within model, intercept (same for all
% 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}.
+% by size(obj.dat,2) x 1 vector of block labels.
+% 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
diff --git a/CanlabCore/@fmridisplay/addpoints.m b/CanlabCore/@fmridisplay/addpoints.m
index 496be742..939646f8 100644
--- a/CanlabCore/@fmridisplay/addpoints.m
+++ b/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;
diff --git a/CanlabCore/@fmridisplay/fmridisplay.m b/CanlabCore/@fmridisplay/fmridisplay.m
index 94514c11..2a349cc5 100644
--- a/CanlabCore/@fmridisplay/fmridisplay.m
+++ b/CanlabCore/@fmridisplay/fmridisplay.m
@@ -29,17 +29,17 @@
% 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]);
@@ -50,7 +50,7 @@
%
% 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]});
@@ -61,7 +61,7 @@
% 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');
diff --git a/CanlabCore/@fmridisplay/montage.m b/CanlabCore/@fmridisplay/montage.m
index e95cf624..ea1655ff 100644
--- a/CanlabCore/@fmridisplay/montage.m
+++ b/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';
diff --git a/CanlabCore/@fmridisplay/zoom_in_on_regions.m b/CanlabCore/@fmridisplay/zoom_in_on_regions.m
index 7c3f9a53..009e8e62 100644
--- a/CanlabCore/@fmridisplay/zoom_in_on_regions.m
+++ b/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, :);
diff --git a/CanlabCore/@image_vector/display_slices.m b/CanlabCore/@image_vector/display_slices.m
index 5f552930..98c77451 100644
--- a/CanlabCore/@image_vector/display_slices.m
+++ b/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));
diff --git a/CanlabCore/@image_vector/slices.m b/CanlabCore/@image_vector/slices.m
index b62b3de1..8744556c 100644
--- a/CanlabCore/@image_vector/slices.m
+++ b/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 = [];
diff --git a/CanlabCore/@statistic_image/multi_threshold.m b/CanlabCore/@statistic_image/multi_threshold.m
index 93db185b..40a0fd9d 100644
--- a/CanlabCore/@statistic_image/multi_threshold.m
+++ b/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
diff --git a/CanlabCore/Cluster_contig_region_tools/Cluster-based_multivar_tools/cluster_nmdsfig.m b/CanlabCore/Cluster_contig_region_tools/Cluster-based_multivar_tools/cluster_nmdsfig.m
index 0e9ab959..e08c31b1 100644
--- a/CanlabCore/Cluster_contig_region_tools/Cluster-based_multivar_tools/cluster_nmdsfig.m
+++ b/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
diff --git a/CanlabCore/Data_extraction/readim2.m b/CanlabCore/Data_extraction/readim2.m
index 72b43df7..de9e88bc 100644
--- a/CanlabCore/Data_extraction/readim2.m
+++ b/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
diff --git a/CanlabCore/ROI_drawing_tools/draw_anatomical_roi.m b/CanlabCore/ROI_drawing_tools/draw_anatomical_roi.m
index 3c88b85b..280ad118 100644
--- a/CanlabCore/ROI_drawing_tools/draw_anatomical_roi.m
+++ b/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
diff --git a/CanlabCore/ROI_drawing_tools/draw_anatomical_roi_2008.m b/CanlabCore/ROI_drawing_tools/draw_anatomical_roi_2008.m
index 30bb202d..5baecc7c 100644
--- a/CanlabCore/ROI_drawing_tools/draw_anatomical_roi_2008.m
+++ b/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',...
diff --git a/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_bestsubsets_brain.m b/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_bestsubsets_brain.m
index 846f586a..f7ecc659 100644
--- a/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_bestsubsets_brain.m
+++ b/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'
diff --git a/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_lasso_brain.m b/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_lasso_brain.m
index 3d08a6a3..1857ced4 100644
--- a/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_lasso_brain.m
+++ b/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'
diff --git a/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_lasso_brain_featureselect.m b/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_lasso_brain_featureselect.m
index 2deba72b..76c97c31 100644
--- a/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_lasso_brain_featureselect.m
+++ b/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'
diff --git a/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_regression_multisubject_bootstrapweightmap.m b/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_regression_multisubject_bootstrapweightmap.m
index 3f177009..5c6bd065 100644
--- a/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_regression_multisubject_bootstrapweightmap.m
+++ b/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)
diff --git a/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_ridge_brain.m b/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_ridge_brain.m
index 04ddfbf2..1f289628 100644
--- a/CanlabCore/Statistics_tools/Cross_validated_Regression/xval_ridge_brain.m
+++ b/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'
diff --git a/CanlabCore/Statistics_tools/canlab_run_paired_SVM.m b/CanlabCore/Statistics_tools/canlab_run_paired_SVM.m
index 8350c1ed..07e3f733 100644
--- a/CanlabCore/Statistics_tools/canlab_run_paired_SVM.m
+++ b/CanlabCore/Statistics_tools/canlab_run_paired_SVM.m
@@ -45,7 +45,7 @@
% Followed by logical 1/0
%
% **boot_n:**
-% Followed by number of boostrap samples desired (default = 100)
+% Followed by number of bootstrap samples desired (default = 100)
%
% **parallelstr:**
% Followed by string 'parallel' to use parallel processing in fmri_data.predict.m
diff --git a/CanlabCore/Statistics_tools/roc_plot.m b/CanlabCore/Statistics_tools/roc_plot.m
index e749fe84..2fcc8dbe 100644
--- a/CanlabCore/Statistics_tools/roc_plot.m
+++ b/CanlabCore/Statistics_tools/roc_plot.m
@@ -595,7 +595,7 @@
ROC.line_handle = han;
end
-% Boostrap, if asked for
+% Bootstrap, if asked for
% -------------------------------------------------------------------------
if doboot
diff --git a/CanlabCore/Statistics_tools/scn_stats_helper_functions.m b/CanlabCore/Statistics_tools/scn_stats_helper_functions.m
index 46984fac..6762bd6f 100644
--- a/CanlabCore/Statistics_tools/scn_stats_helper_functions.m
+++ b/CanlabCore/Statistics_tools/scn_stats_helper_functions.m
@@ -16,7 +16,7 @@
% unweighted; with AR model if specified as last input
%
% **'boot':**
-% Boostrapping of GLS
+% Bootstrapping of GLS
%
% **'signperm':**
% Sign permutation test for intercept of GLS
@@ -1263,7 +1263,7 @@ function loess_partial(M, Y, X, varargin)
[final_boot_samples, alphaaccept] = get_boot_samples_needed(stats.p, whpvals_for_boot, targetu, bootsamples, verbose); % uses whpvals_for_boot, returns Be
-% set up boostrap beta-generating function
+% set up bootstrap beta-generating function
% generic for multiple cols of Y (outcomes), multiple cols. of X
% (predictors), weights equal or not (W)
% much faster if X is intercept only!
diff --git a/CanlabCore/Visualization_functions/canlab_results_fmridisplay.m b/CanlabCore/Visualization_functions/canlab_results_fmridisplay.m
index 86390486..7b2f89c0 100644
--- a/CanlabCore/Visualization_functions/canlab_results_fmridisplay.m
+++ b/CanlabCore/Visualization_functions/canlab_results_fmridisplay.m
@@ -54,10 +54,10 @@
% options to specify to enable the necessary transformations. Otherwise naive sampling based on naive surface
% vertex coordinates will be used, which in most cases will not correctly map to your data volume.
%
-% 'full' Axial, coronal, and saggital slices, 4 cortical surfaces
-% 'compact' Midline saggital and two rows of axial slices [the default]
-% 'compact2' A single row showing midline saggital and axial slices
-% 'compact3' One row of axial slices, midline sagg, and 4 HCP surfaces
+% 'full' Axial, coronal, and sagittal slices, 4 cortical surfaces
+% 'compact' Midline sagittal and two rows of axial slices [the default]
+% 'compact2' A single row showing midline sagittal and axial slices
+% 'compact3' One row of axial slices, midline sagit, and 4 HCP surfaces
% 'multirow' A series of 'compact2' displays in one figure for comparing different images/maps side by side
% 'regioncenters' A series of separate axes, each focused on one region
% 'full2' for a slightly less full montage that avoids colorbar overlap issues
@@ -364,7 +364,7 @@
wh = strcmp(varargin, 'coronal');
if any(wh), montagetype = varargin{find(wh)}; varargin(wh) = []; end
-wh = strcmp(varargin, 'saggital');
+wh = strcmp(varargin, 'sagittal');
if any(wh), montagetype = varargin{find(wh)}; varargin(wh) = []; end
wh = strcmp(varargin, 'allslices');
@@ -389,11 +389,11 @@
if any(wh), montagetype = varargin{find(wh)}; varargin(wh) = []; end
-% if these are run before coronal/saggital arguments are parsed they will
+% if these are run before coronal/sagittal arguments are parsed they will
% overwrite the blob/regioncenters argument, so run these last.
wh = strcmp(varargin, 'blobcenters');
if any(wh)
- if ismember(montagetype,{'coronal','saggital'})
+ if ismember(montagetype,{'coronal','sagittal'})
orientation = montagetype;
end
montagetype = varargin{find(wh)};
@@ -402,7 +402,7 @@
wh = strcmp(varargin, 'regioncenters');
if any(wh)
- if ismember(montagetype,{'coronal','saggital'})
+ if ismember(montagetype,{'coronal','sagittal'})
orientation = montagetype;
end
montagetype = varargin{find(wh)};
@@ -522,20 +522,20 @@
case 'compact'
% The default
- % saggital
+ % sagittal
axh1 = axes('Position', [-0.02 0.4 .17 .17]);
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', [-4 0 0], 'onerow', 'noverbose', 'existing_axes', axh1);
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', [-4 0 0], 'onerow', 'noverbose', 'existing_axes', axh1);
text(50, -50, 'left');
drawnow
axh2 = axes('Position', [-0.02 0.6 .17 .17]);
- o2 = montage(o2, 'volume_data', dat, 'saggital', 'wh_slice', [4 0 0], 'onerow', 'noverbose', 'existing_axes', axh2);
+ o2 = montage(o2, 'volume_data', dat, 'sagittal', 'wh_slice', [4 0 0], 'onerow', 'noverbose', 'existing_axes', axh2);
text(50, -50, 'right');
drawnow
% sagg center
axh3 = axes('Position', [.08 0.5 .17 .17]);
- o2 = montage(o2, 'volume_data', dat, 'saggital', 'wh_slice', [0 0 0], 'onerow', 'noverbose', 'existing_axes', axh3);
+ o2 = montage(o2, 'volume_data', dat, 'sagittal', 'wh_slice', [0 0 0], 'onerow', 'noverbose', 'existing_axes', axh3);
drawnow;
o2.montage{3}.slice_mm_coords;
@@ -632,15 +632,15 @@
end
- % saggital
+ % sagittal
axh = axes('Position', [-0.02 .75-shiftvals(i) .17 .17]); % [-0.02 0.15+shiftvals(i) .17 .17]);
axh(2) = axes('Position', [.022 .854-shiftvals(i) .17 .17]);
if i == 1
- [o2, dat] = montage(o2, 'saggital', 'slice_range', [-2 2], 'spacing', 4, 'onerow', 'noverbose', 'existing_axes', axh);
+ [o2, dat] = montage(o2, 'sagittal', 'slice_range', [-2 2], 'spacing', 4, 'onerow', 'noverbose', 'existing_axes', axh);
else
- o2 = montage(o2, 'volume_data', dat, 'saggital', 'slice_range', [-2 2], 'spacing', 4, 'onerow', 'noverbose', 'existing_axes', axh);
+ o2 = montage(o2, 'volume_data', dat, 'sagittal', 'slice_range', [-2 2], 'spacing', 4, 'onerow', 'noverbose', 'existing_axes', axh);
end
drawnow
@@ -697,10 +697,11 @@
end
case 'full'
- % --- Saggital ---
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', xyz, 'onerow', 'noverbose');
+
+ % sagittal
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', xyz, 'onerow', 'noverbose');
shift_axes(-0.02, -0.04);
- sag_coords = xyz(:, 1); % x-coordinates for saggital
+ sag_coords = xyz(:, 1); % x-coordinates for sagittal
% --- Coronal ---
sr_cor = [-40 50];
@@ -785,8 +786,8 @@
case 'full2'
- % saggital
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', xyz, 'onerow', 'noverbose');
+ % sagittal
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', xyz, 'onerow', 'noverbose');
shift_axes(-0.02, -0.04);
% coronal
@@ -880,7 +881,7 @@
axh = axes('Position', [-0.06 .75-.34 .29 .29]); % [-0.02 0.15+shiftvals(i) .17 .17]);
axh(2) = axes('Position', [-0.02 .854-.27 .29 .29]);
- o2 = montage(o2, 'volume_data', dat, 'saggital', 'slice_range', [-2 2], 'spacing', 4, 'onerow', 'noverbose', 'existing_axes', axh);
+ o2 = montage(o2, 'volume_data', dat, 'sagittal', 'slice_range', [-2 2], 'spacing', 4, 'onerow', 'noverbose', 'existing_axes', axh);
% --- Coordinate Annotation Overlay ---
if coordinates
@@ -953,13 +954,14 @@
set(allaxh(i), 'Position', pos1);
end
+
enlarge_axes(gcf, 1);
- % Medial sagg slices
+ % Medial sag slices
axh = axes('Position', [-0.06 .75-.34 .29 .29]); % [-0.02 0.15+shiftvals(i) .17 .17]);
axh(2) = axes('Position', [-0.02 .854-.27 .29 .29]);
- o2 = montage(o2, 'volume_data', dat, 'saggital', 'slice_range', [-2 2], 'spacing', 4, 'onerow', 'noverbose', 'existing_axes', axh);
+ o2 = montage(o2, 'volume_data', dat, 'sagittal', 'slice_range', [-2 2], 'spacing', 4, 'onerow', 'noverbose', 'existing_axes', axh);
% --- Coordinate Annotation Overlay ---
if coordinates
@@ -1055,7 +1057,7 @@
end
end
- case {'saggital', 'sagittal'}
+ case {'sagittal'}
o2 = montage(o2, montagetype, 'wh_slice', xyz, 'onerow', 'noverbose');
wh_montages = 1;
@@ -1092,7 +1094,8 @@
case 'allslices'
% --- Sagittal montage ---
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', xyz, 'onerow', 'noverbose');
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', xyz, 'onerow', 'noverbose');
+
shift_axes(-0.02, -0.04);
sag_coords = xyz(:, 1); % x-coordinates
@@ -1136,8 +1139,8 @@
wh_montages = [1 2 3];
case 'full hcp'
- % saggital
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', xyz, 'onerow', 'noverbose');
+ % sagittal
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', xyz, 'onerow', 'noverbose');
shift_axes(-0.02, -0.04);surface right
% coronal
@@ -1151,6 +1154,11 @@
axh = axes('Position', [-0.02 0.01 .17 .17]);
o2 = montage(o2, 'volume_data', dat, 'axial', 'slice_range', [-44 50], 'onerow', 'spacing', 8, 'noverbose', 'existing_axes', axh);
+ case 'full hcp'
+
+ % sagittal
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', xyz, 'onerow', 'noverbose');
+
allaxh = findobj(gcf, 'Type', 'axes');
disp(length(allaxh));
for i = 1:(length(allaxh)-36)
@@ -1217,8 +1225,9 @@
case 'full hcp inflated'
- % saggital
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', xyz, 'onerow', 'noverbose');
+ % sagittal
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', xyz, 'onerow', 'noverbose');
+
shift_axes(-0.02, -0.04);
% coronal
@@ -1297,8 +1306,8 @@
case 'full no surfaces'
- % saggital
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', xyz, 'onerow', 'noverbose');
+ % sagittal
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', xyz, 'onerow', 'noverbose');
% shift_axes(-0.02, -0.04);
% coronal
@@ -1369,7 +1378,7 @@
wh_montages = [1 2 3 4];
case 'hcp grayordinates'
- % saggital
+ % sagittal
f1 = gcf;
mainLayout = tiledlayout(f1,1,5);
surfLayout = tiledlayout(mainLayout, 2, 2, 'Parent', mainLayout, 'TileSpacing', 'compact', 'Padding', 'none');
@@ -1391,7 +1400,8 @@
volLayout.Layout.TileSpan = [1, 3]; % Span three tiles
ax_vol=[];
for j = 1:n_row, for k = 1:n_col, ax_vol(j,k) = nexttile(volLayout); end; end
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', grayord_xyz, 'onerow', 'noverbose', 'existing_axes',ax_vol(1,:));
+
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', grayord_xyz, 'onerow', 'noverbose', 'existing_axes',ax_vol(1,:));
for j=1:n_col
set(ax_vol(1,j),'XLim',[-100,30],'YLim',[-70,25]);
title(ax_vol(1,j), sprintf('x=%.0f', grayord_xyz(j,1)), 'FontSize', 10);
@@ -1415,14 +1425,14 @@
wh_surfaces = [1:4];
case 'hcp grayordinates subcortex'
- % saggital
+ % sagittal
f1 = gcf;
n_col = size(grayord_xyz,1);
n_row = size(grayord_xyz,2);
volLayout = tiledlayout(f1, n_row, n_col, 'TileSpacing', 'tight', 'Padding', 'none');
ax_vol=[];
for j = 1:n_row, for k = 1:n_col, ax_vol(j,k) = nexttile(volLayout); end; end
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', grayord_xyz, 'onerow', 'noverbose', 'existing_axes',ax_vol(1,:));
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', grayord_xyz, 'onerow', 'noverbose', 'existing_axes',ax_vol(1,:));
for j=1:n_col, set(ax_vol(1,j),'XLim',[-100,30],'YLim',[-70,25]); end
% coronal
@@ -1520,9 +1530,9 @@
t8.Layout.Tile = 24;
axis off
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', grayord_xyz(1,:), 'onerow', 'noverbose', 'existing_axes',t5);
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', grayord_xyz(3,:), 'onerow', 'noverbose', 'existing_axes',t6);
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', grayord_xyz(5,:), 'onerow', 'noverbose', 'existing_axes',t7);
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', grayord_xyz(1,:), 'onerow', 'noverbose', 'existing_axes',t5);
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', grayord_xyz(3,:), 'onerow', 'noverbose', 'existing_axes',t6);
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', grayord_xyz(5,:), 'onerow', 'noverbose', 'existing_axes',t7);
[o2, dat] = montage(o2, 'axial', 'wh_slice', grayord_xyz(2,:), 'onerow', 'noverbose', 'existing_axes',t8);
title(t5,'X = -24','FontSize',10)
@@ -1576,9 +1586,9 @@
t8.Layout.Tile = 24;
axis off
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', grayord_xyz(1,:), 'onerow', 'noverbose', 'existing_axes',t5);
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', grayord_xyz(3,:), 'onerow', 'noverbose', 'existing_axes',t6);
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', grayord_xyz(5,:), 'onerow', 'noverbose', 'existing_axes',t7);
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', grayord_xyz(1,:), 'onerow', 'noverbose', 'existing_axes',t5);
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', grayord_xyz(3,:), 'onerow', 'noverbose', 'existing_axes',t6);
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', grayord_xyz(5,:), 'onerow', 'noverbose', 'existing_axes',t7);
[o2, dat] = montage(o2, 'axial', 'wh_slice', grayord_xyz(2,:), 'onerow', 'noverbose', 'existing_axes',t8);
title(t5,'X = -24','FontSize',10)
@@ -1593,7 +1603,7 @@
wh_surfaces = [1:4];
case 'leftright inout subcortex'
- % saggital
+ % sagittal
f1 = gcf;
mainLayout = tiledlayout(f1,1,5);
surfLayout = tiledlayout(mainLayout, 2, 2, 'Parent', mainLayout, 'TileSpacing', 'compact', 'Padding', 'none');
@@ -1614,7 +1624,7 @@
volLayout.Layout.TileSpan = [1, 3];
ax_vol=[];
for j = 1:n_row, for k = 1:n_col, ax_vol(j,k) = nexttile(volLayout); end; end
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', grayord_xyz, 'onerow', 'noverbose', 'existing_axes',ax_vol(1,:));
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', grayord_xyz, 'onerow', 'noverbose', 'existing_axes',ax_vol(1,:));
for j=1:n_col
set(ax_vol(1,j),'XLim',[-100,30],'YLim',[-70,25]);
title(ax_vol(1,j), sprintf('x=%.0f', grayord_xyz(j,1)), 'FontSize', 10);
@@ -1637,7 +1647,7 @@
case 'subcortex full'
- % saggital
+ % sagittal
f1 = gcf;
mainLayout = tiledlayout(f1,1,5);
surfLayout = tiledlayout(mainLayout, 2, 2, 'Parent', mainLayout, 'TileSpacing', 'compact', 'Padding', 'none');
@@ -1658,7 +1668,7 @@
volLayout.Layout.TileSpan = [1, 3];
ax_vol=[];
for j = 1:n_row, for k = 1:n_col, ax_vol(j,k) = nexttile(volLayout); end; end
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', grayord_xyz, 'onerow', 'noverbose', 'existing_axes',ax_vol(1,:));
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', grayord_xyz, 'onerow', 'noverbose', 'existing_axes',ax_vol(1,:));
for j=1:n_col
set(ax_vol(1,j),'XLim',[-100,30],'YLim',[-70,25]);
title(ax_vol(1,j), sprintf('x=%.0f', grayord_xyz(j,1)), 'FontSize', 10);
@@ -1691,7 +1701,7 @@
volLayout.Layout.TileSpan = [1, 3];
ax_vol=[];
for j = 1:n_row, for k = 1:n_col, ax_vol(j,k) = nexttile(volLayout); end; end
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', grayord_xyz, 'onerow', 'noverbose', 'existing_axes',ax_vol(1,:));
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', grayord_xyz, 'onerow', 'noverbose', 'existing_axes',ax_vol(1,:));
for j=1:n_col
set(ax_vol(1,j),'XLim',[-100,30],'YLim',[-70,25]);
title(ax_vol(1,j), sprintf('x=%.0f', grayord_xyz(j,1)), 'FontSize', 10);
@@ -1866,8 +1876,9 @@
% use same o2, but add montages
switch montagetype
case 'full'
- % saggital
- [o2, dat] = montage(o2, 'saggital', 'wh_slice', xyz, 'onerow', 'noverbose');
+
+ % sagittal
+ [o2, dat] = montage(o2, 'sagittal', 'wh_slice', xyz, 'onerow', 'noverbose');
shift_axes(-0.02, -0.04);
% coronal
@@ -1946,7 +1957,8 @@
case 'compact'
[o2, dat] = montage(o2, 'axial', 'slice_range', [-40 50], 'onerow', 'spacing', 6, 'noverbose');
axh = axes('Position', [0.05 0.4 .1 .5]);
- o2 = montage(o2, 'volume_data', dat, 'saggital', 'wh_slice', [0 0 0], 'existing_axes', axh, 'noverbose');
+
+ o2 = montage(o2, 'volume_data', dat, 'sagittal', 'wh_slice', [0 0 0], 'existing_axes', axh, 'noverbose');
% --- Apply coordinate titles if coordinates flag is on ---
if coordinates
@@ -1992,7 +2004,7 @@
[o2, dat] = montage(o2, 'axial', 'slice_range', [-40 50], 'onerow', 'spacing', 8, 'noverbose');
enlarge_axes(gcf, 1);
axh = axes('Position', [-0.03 0.15 .2 1]);
- o2 = montage(o2, 'volume_data', dat, 'saggital', 'wh_slice', [0 0 0], 'existing_axes', axh, 'noverbose');
+ o2 = montage(o2, 'volume_data', dat, 'sagittal', 'wh_slice', [0 0 0], 'existing_axes', axh, 'noverbose');
% shift all axes down and right
shift_axes(+0.03, -0.10);
diff --git a/CanlabCore/Visualization_functions/cluster_orthviews_classes.m b/CanlabCore/Visualization_functions/cluster_orthviews_classes.m
index ae2e1381..0da44eb7 100644
--- a/CanlabCore/Visualization_functions/cluster_orthviews_classes.m
+++ b/CanlabCore/Visualization_functions/cluster_orthviews_classes.m
@@ -36,7 +36,7 @@
%
% classes = c.ClusterSolution.classes;
% overlay = EXPT.overlay;
-% cluster_orthviews_classes(cl,c.ClusterSolution.classes, EXPT.overlay, 'saggital', 0);
+% cluster_orthviews_classes(cl,c.ClusterSolution.classes, EXPT.overlay, 'sagittal', 0);
% cluster_orthviews_classes(cl,c.ClusterSolution.classes, EXPT.overlay, 'axial', 0);
% cluster_orthviews_classes(cl,c.ClusterSolution.classes, EXPT.overlay, 'coronal', 0);
% cluster_orthviews_classes(cl,c.ClusterSolution.classes, EXPT.overlay, [], 0);
diff --git a/CanlabCore/Visualization_functions/cluster_orthviews_montage.m b/CanlabCore/Visualization_functions/cluster_orthviews_montage.m
index 66117b82..69d07076 100644
--- a/CanlabCore/Visualization_functions/cluster_orthviews_montage.m
+++ b/CanlabCore/Visualization_functions/cluster_orthviews_montage.m
@@ -332,7 +332,7 @@
axish(other_axes) = [];
poss(other_axes, :) = [];
-% sort into order: axial, coronal, saggital
+% sort into order: axial, coronal, sagittal
ssum = sum(poss(:, 1:2), 2);
[ssum, ind] = sort(ssum);
axish = axish(ind);
diff --git a/CanlabCore/Visualization_functions/cluster_orthviews_showcenters.m b/CanlabCore/Visualization_functions/cluster_orthviews_showcenters.m
index 573dbe52..58286320 100644
--- a/CanlabCore/Visualization_functions/cluster_orthviews_showcenters.m
+++ b/CanlabCore/Visualization_functions/cluster_orthviews_showcenters.m
@@ -145,7 +145,7 @@
axish(other_axes) = [];
poss(other_axes, :) = [];
- % sort into order: axial, coronal, saggital
+ % sort into order: axial, coronal, sagittal
ssum = sum(poss(:, 1:2), 2);
[ssum, ind] = sort(ssum);
axish = axish(ind);
diff --git a/CanlabCore/Visualization_functions/conf_region.m b/CanlabCore/Visualization_functions/conf_region.m
index 42cd124c..20497cce 100644
--- a/CanlabCore/Visualization_functions/conf_region.m
+++ b/CanlabCore/Visualization_functions/conf_region.m
@@ -70,7 +70,7 @@
% %create_figure('test');
% [h,h2] = plot_ellipse(cen(1),cen(2),theta,ci(1,1),ci(2,2));
%
-% % plot standard deviation - for boostrapping, or for individual cases
+% % plot standard deviation - for bootstrapping, or for individual cases
% [h,h2] = plot_ellipse(cen(1),cen(2),theta,ci(1,1)*sqrt(N),ci(2,2)*sqrt(N));
%
% :Example: Render individual subject conf regions
diff --git a/CanlabCore/Visualization_functions/make_figure_into_orthviews.m b/CanlabCore/Visualization_functions/make_figure_into_orthviews.m
index 5187860f..d46f6855 100644
--- a/CanlabCore/Visualization_functions/make_figure_into_orthviews.m
+++ b/CanlabCore/Visualization_functions/make_figure_into_orthviews.m
@@ -5,7 +5,7 @@
% [hh1,hh2,hh3,hl,a1,a2,a3] = make_figure_into_orthviews
%
% Copies a surface rendering or glass brain into three separate view
-% panels, one saggital, one axial, and one coronal
+% panels, one sagittal, one axial, and one coronal
%
% returns handles to objects in each view and hl light handles
%
diff --git a/CanlabCore/Visualization_functions/riverplot/riverplot_draw_layer.m b/CanlabCore/Visualization_functions/riverplot/riverplot_draw_layer.m
index 70192bf4..f328199e 100644
--- a/CanlabCore/Visualization_functions/riverplot/riverplot_draw_layer.m
+++ b/CanlabCore/Visualization_functions/riverplot/riverplot_draw_layer.m
@@ -33,7 +33,7 @@
% :Inputs:
%
% **rect1:**
-% Structure with handles and decription of imrect class object,
+% Structure with handles and description of imrect class object,
% created with riverplot_rect.m. This is always the LEFTMOST
% rect of the pair.
%
diff --git a/CanlabCore/Visualization_functions/riverplot/riverplot_draw_ribbon.m b/CanlabCore/Visualization_functions/riverplot/riverplot_draw_ribbon.m
index a0e8a7f5..f7c4724c 100644
--- a/CanlabCore/Visualization_functions/riverplot/riverplot_draw_ribbon.m
+++ b/CanlabCore/Visualization_functions/riverplot/riverplot_draw_ribbon.m
@@ -33,7 +33,7 @@
% :Inputs:
%
% **rect1:**
-% Structure with handles and decription of imrect class object,
+% Structure with handles and description of imrect class object,
% created with riverplot_rect.m. This is always the LEFTMOST
% rect of the pair.
%
diff --git a/CanlabCore/Visualization_functions/riverplot/riverplot_layer_names.m b/CanlabCore/Visualization_functions/riverplot/riverplot_layer_names.m
index 32e04a44..0e221778 100644
--- a/CanlabCore/Visualization_functions/riverplot/riverplot_layer_names.m
+++ b/CanlabCore/Visualization_functions/riverplot/riverplot_layer_names.m
@@ -32,7 +32,7 @@
% :Inputs:
%
% **layerstruct:**
-% Structure with handles and decription of imrect class objects for
+% Structure with handles and description of imrect class objects for
% a layer. Layerstruct is created with riverplot_draw_layer.
%
% **layernames:**
diff --git a/CanlabCore/Visualization_functions/riverplot/riverplot_ribbon.m b/CanlabCore/Visualization_functions/riverplot/riverplot_ribbon.m
index 32e5577d..28e1ebcb 100644
--- a/CanlabCore/Visualization_functions/riverplot/riverplot_ribbon.m
+++ b/CanlabCore/Visualization_functions/riverplot/riverplot_ribbon.m
@@ -33,7 +33,7 @@
% :Inputs:
%
% **rect1:**
-% Structure with handles and decription of imrect class object,
+% Structure with handles and description of imrect class object,
% created with riverplot_rect.m. This is always the LEFTMOST
% rect of the pair.
%
diff --git a/CanlabCore/Visualization_functions/riverplot/riverplot_ribbon_matrix.m b/CanlabCore/Visualization_functions/riverplot/riverplot_ribbon_matrix.m
index a566ff44..a99aac2b 100644
--- a/CanlabCore/Visualization_functions/riverplot/riverplot_ribbon_matrix.m
+++ b/CanlabCore/Visualization_functions/riverplot/riverplot_ribbon_matrix.m
@@ -34,7 +34,7 @@
% :Inputs:
%
% **layer1:**
-% Cell array of structures with handles and decription of imrect class objects,
+% Cell array of structures with handles and description of imrect class objects,
% created with riverplot_draw_layer.m. Each object is a rectangular
% graphic that denotes a spatial brain pattern or mask created with riverplot_rect.m.
% layer1 is the LEFTMOST layer in the plot.
diff --git a/CanlabCore/Visualization_functions/roi_contour_map.m b/CanlabCore/Visualization_functions/roi_contour_map.m
index cb1d1496..b823ca5a 100644
--- a/CanlabCore/Visualization_functions/roi_contour_map.m
+++ b/CanlabCore/Visualization_functions/roi_contour_map.m
@@ -1,5 +1,5 @@
function info = roi_contour_map(dat, varargin)
-% Draw a pattern map of one slice (either saggital, axial, or coronal) that
+% Draw a pattern map of one slice (either sagittal, axial, or coronal) that
% shows the most voxels, or the slice that you specify (e.g., x = #).
% You can also draw outlines for the significant voxels from a statistical test.
%
@@ -64,7 +64,7 @@
%
% **'xyz':**
% When you want a specific view and slice, you can use this
-% option with 'coord'. (1:x - saggital view, 2:y - coronal
+% option with 'coord'. (1:x - sagittal view, 2:y - coronal
% view, 3:z - axial view)
%
% **'coord':**
@@ -94,7 +94,7 @@
% info.dat:
% - [2x30 double] (xyz mesh)
% - Z: [1x30 double] (z values)
-% - xyz: 3 (1:x-saggital, 2:y-coronal, 3:z-axial)
+% - xyz: 3 (1:x-sagittal, 2:y-coronal, 3:z-axial)
% - xyz_coord: -2 (slice coordinate; in this case, z = 3)
% - region_idx: 1
%
diff --git a/CanlabCore/Visualization_functions/spm_orthviews_showposition.m b/CanlabCore/Visualization_functions/spm_orthviews_showposition.m
index d02aeefa..bea9b37c 100644
--- a/CanlabCore/Visualization_functions/spm_orthviews_showposition.m
+++ b/CanlabCore/Visualization_functions/spm_orthviews_showposition.m
@@ -34,7 +34,7 @@
% coronal
h(2) = put_text(axish(2),['y = ' num2str(pos(2))]);
- % saggital
+ % sagittal
h(3) = put_text(axish(3),['x = ' num2str(pos(1))]);
end
@@ -64,7 +64,7 @@
% % axish(other_axes) = [];
% % poss(other_axes,:) = [];
% %
- % % % sort into order: axial, coronal, saggital
+ % % % sort into order: axial, coronal, sagittal
% % ssum = sum(poss(:,1:2),2);
% % [ssum,ind] = sort(ssum);
% % axish = axish(ind);
@@ -76,7 +76,7 @@
% % % coronal
% % h(2) = put_text(axish(2),['y = ' num2str(pos(2))]);
% %
- % % % saggital
+ % % % sagittal
% % h(3) = put_text(axish(3),['x = ' num2str(pos(1))]);
diff --git a/CanlabCore/Visualization_functions/tor_ihb_TalSpace.m b/CanlabCore/Visualization_functions/tor_ihb_TalSpace.m
index 50923df7..b4293389 100644
--- a/CanlabCore/Visualization_functions/tor_ihb_TalSpace.m
+++ b/CanlabCore/Visualization_functions/tor_ihb_TalSpace.m
@@ -68,12 +68,12 @@ function tor_ihb_TalSpace()
%
% axes hAxAxial axial
% axes hAxFront frontal
-% axes hAxSagL left saggital
-% axes hAxSagR right saggital
+% axes hAxSagL left sagittal
+% axes hAxSagR right sagittal
% strucure array clusters array of selected clusters
% integer indClusterToView index of currently viewed cluster in clusters array
-% bool drawSymLS == 1 if draw symmetrical on left saggital
-% bool drawSymRS == 1 if draw symmetrical on right saggital
+% bool drawSymLS == 1 if draw symmetrical on left sagittal
+% bool drawSymRS == 1 if draw symmetrical on right sagittal
%
%----------------------------------------------------------------------------------
%
diff --git a/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/create_anatomical_underlay_2016.m b/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/create_anatomical_underlay_2016.m
index 4f04f394..bcb030da 100644
--- a/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/create_anatomical_underlay_2016.m
+++ b/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/create_anatomical_underlay_2016.m
@@ -71,9 +71,9 @@
o2 = fmridisplay('overlay', which(imgs{i}));
- % saggital
+ % sagittal
axh = axes('Position', [-0.02 0.15+shiftvals(i) .17 .17]);
- o2 = montage(o2, 'saggital', 'wh_slice', [0 0 0], 'onerow', 'noverbose', 'existing_axes', axh);
+ o2 = montage(o2, 'sagittal', 'wh_slice', [0 0 0], 'onerow', 'noverbose', 'existing_axes', axh);
drawnow
% axial
diff --git a/CanlabCore/canlab_canonical_brains/Cortical_ROI_masks/insula_ribbon_partial_script.m b/CanlabCore/canlab_canonical_brains/Cortical_ROI_masks/insula_ribbon_partial_script.m
index a67eee1d..dd533fc1 100644
--- a/CanlabCore/canlab_canonical_brains/Cortical_ROI_masks/insula_ribbon_partial_script.m
+++ b/CanlabCore/canlab_canonical_brains/Cortical_ROI_masks/insula_ribbon_partial_script.m
@@ -1,4 +1,4 @@
-% procedure: use draw_anatomical_ROI_2008 to draw saggital slices
+% procedure: use draw_anatomical_ROI_2008 to draw sagittal slices
% then mask with cortical ribbon from segmentation
% then clean up using draw...
diff --git a/CanlabCore/diagnostics/displayme.m b/CanlabCore/diagnostics/displayme.m
index 1dd4156e..2ea88d7e 100644
--- a/CanlabCore/diagnostics/displayme.m
+++ b/CanlabCore/diagnostics/displayme.m
@@ -1,6 +1,6 @@
function [subjM,Mtotalv] = displayme(mm,txtlab,tlab2)
% Used in img_hist2 - included as internal function there.
-% this function is for indepenent re-display after img_hist2 is finished.
+% this function is for independent re-display after img_hist2 is finished.
%
% :Usage:
% ::
diff --git a/CanlabCore/mlpcr/mlpcr2.m b/CanlabCore/mlpcr/mlpcr2.m
index 6110ab46..edc406f8 100644
--- a/CanlabCore/mlpcr/mlpcr2.m
+++ b/CanlabCore/mlpcr/mlpcr2.m
@@ -21,7 +21,7 @@
% If the defaults are used then the result is identical to PCR, only you
% get both within and between subject predictive models in addition to the
% full model. Different results may be obtained with hyperparameter
-% optimization or concensus PCA enabled.
+% optimization or consensus PCA enabled.
%
%
% Input ::
@@ -53,9 +53,9 @@
% default if you wish to treat trait differences as
% noise.
%
-% 'cpca' - followed by 0/1 to indicate whether or not concensus PCA
+% 'cpca' - followed by 0/1 to indicate whether or not consensus PCA
% (Westerhuis, et al. 1998) should be used in place of
-% standard pca. If concensus PCA is enabled eigenvectors
+% standard pca. If consensus PCA is enabled eigenvectors
% will be selected such that variance is explained
% equally across all blocks. Otherwise eigenvectors will
% best represent blocks with the most observations.
@@ -65,7 +65,7 @@
% and will consequently fight against CPCA. A future
% update may fix this, and if so this note should be
% removed.
-% Note 2: In principle concensus PCA could be implemened
+% Note 2: In principle consensus PCA could be implemened
% for traditional PCR too. It just hasn't been.
%
% Output ::
@@ -124,7 +124,7 @@
% (allowing the user to force retention of one or the other even if
% eigenvalue rank doesn't justify it)
% - passthrough options to higher level cv_mlpcr, cv_mlpcr_bt and
-% cv_mlpcr_wi scripts. Concensus PCA should also use concensus cv_err,
+% cv_mlpcr_wi scripts. Consensus PCA should also use consensus cv_err,
% cv_mlpcr_wi and cv_mlpcr_bt should have within and between priority
% (respectively) by default.
@@ -192,7 +192,7 @@
end
- % Get concensus PCA solution, which weighs each block equally
+ % Get consensus PCA solution, which weighs each block equally
% requires Matlab 2016b or later perform operation across all
% columns like this with sf
[pc_w,~,~] = svd((sf.*Xw)', 'econ');
diff --git a/CanlabCore/mlpcr/mlpcr3.m b/CanlabCore/mlpcr/mlpcr3.m
index eb98df70..61b387ce 100644
--- a/CanlabCore/mlpcr/mlpcr3.m
+++ b/CanlabCore/mlpcr/mlpcr3.m
@@ -21,7 +21,7 @@
% If the defaults are used then the result is identical to PCR, only you
% get both within and between subject predictive models in addition to the
% full model. Different results may be obtained with hyperparameter
-% optimization or concensus PCA enabled.
+% optimization or consensus PCA enabled.
%
% Input ::
%
@@ -52,9 +52,9 @@
% default if you wish to treat trait differences as
% noise.
%
-% 'cpca' - followed by 0/1 to indicate whether or not concensus PCA
+% 'cpca' - followed by 0/1 to indicate whether or not consensus PCA
% (Westerhuis, et al. 1998) should be used in place of
-% standard pca. If concensus PCA is enabled eigenvectors
+% standard pca. If consensus PCA is enabled eigenvectors
% will be selected such that variance is explained
% equally across all blocks. Otherwise eigenvectors will
% best represent blocks with the most observations.
@@ -64,7 +64,7 @@
% and will consequently fight against CPCA. A future
% update may fix this, and if so this note should be
% removed.
-% Note 2: In principle concensus PCA could be implemened
+% Note 2: In principle consensus PCA could be implemened
% for traditional PCR too. It just hasn't been.
%
% 'randInt' - Fit a random intercept model. Default=false
@@ -129,7 +129,7 @@
% (allowing the user to force retention of one or the other even if
% eigenvalue rank doesn't justify it)
% - passthrough options to higher level cv_mlpcr, cv_mlpcr_bt and
-% cv_mlpcr_wi scripts. Concensus PCA should also use concensus cv_err,
+% cv_mlpcr_wi scripts. Consensus PCA should also use consensus cv_err,
% cv_mlpcr_wi and cv_mlpcr_bt should have within and between priority
% (respectively) by default.
@@ -224,7 +224,7 @@
end
- % Get concensus PCA solution, which weighs each block equally
+ % Get consensus PCA solution, which weighs each block equally
% requires Matlab 2016b or later perform operation across all
% columns like this with sf
[pc_w,~,~] = svd((sf.*Xw)', 'econ');
diff --git a/CanlabCore/web_repository_tools/test_pattern_on_kragel_2018_n270_data.m b/CanlabCore/web_repository_tools/test_pattern_on_kragel_2018_n270_data.m
index 937b44d7..862b9de4 100644
--- a/CanlabCore/web_repository_tools/test_pattern_on_kragel_2018_n270_data.m
+++ b/CanlabCore/web_repository_tools/test_pattern_on_kragel_2018_n270_data.m
@@ -163,7 +163,7 @@
iscog=iscog(~wh_isnan);
isemo=isemo(~wh_isnan);
-% Boostrap confidence intervals for effect size
+% Bootstrap confidence intervals for effect size
fprintf('Bootstrapping CIs\n')
bci_pain = bootci(5000, @cohens_d_2sample, vector_data, ispain);
diff --git a/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/fmridata.doctree b/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/fmridata.doctree
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diff --git a/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/moduleslist.doctree b/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/moduleslist.doctree
index a84d2b74..c64a012b 100644
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diff --git a/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/oo_tools.doctree b/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/oo_tools.doctree
index b13e49bd..c11a63d0 100644
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diff --git a/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/toolboxes.doctree b/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/toolboxes.doctree
index 067809ee..2d976688 100644
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diff --git a/docs_sphinx_old/SPHINX_DOCS/_build/html/fmridata.html b/docs_sphinx_old/SPHINX_DOCS/_build/html/fmridata.html
index f67bf844..eae5aef5 100644
--- a/docs_sphinx_old/SPHINX_DOCS/_build/html/fmridata.html
+++ b/docs_sphinx_old/SPHINX_DOCS/_build/html/fmridata.html
@@ -701,7 +701,7 @@ Navigation
-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
for timeseries data with stationary autocorrelation.
diff --git a/docs_sphinx_old/SPHINX_DOCS/_build/html/misc_tools.html b/docs_sphinx_old/SPHINX_DOCS/_build/html/misc_tools.html
index ab396ee3..58c4e938 100644
--- a/docs_sphinx_old/SPHINX_DOCS/_build/html/misc_tools.html
+++ b/docs_sphinx_old/SPHINX_DOCS/_build/html/misc_tools.html
@@ -639,7 +639,7 @@ Miscellaneous Tools
sagg:
-to rotate to saggital view
+to rotate to sagittal view
cor:
to rotate to coronal view
@@ -13668,7 +13668,7 @@ Statistics_tools