From f7e37e26b503f3869a08433cecd6944330e4c64f Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 27 Apr 2023 09:51:45 -0400 Subject: [PATCH 1/9] Add github action to codespell master on push and PRs --- .github/workflows/codespell.yml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 .github/workflows/codespell.yml 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 From 0d83fce70270606cb3bf1ba39b7b3fe9bd1095dd Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 27 Apr 2023 09:51:45 -0400 Subject: [PATCH 2/9] Add rudimentary codespell config --- .codespellrc | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 .codespellrc diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 00000000..9ec0d7c4 --- /dev/null +++ b/.codespellrc @@ -0,0 +1,4 @@ +[codespell] +skip = .git,*.pdf,*.svg +# +# ignore-words-list = From c2ae67dd21d129967c92c677aff6330d67722db7 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 28 Nov 2023 15:24:22 -0500 Subject: [PATCH 3/9] ignores --- .codespellrc | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.codespellrc b/.codespellrc index 9ec0d7c4..f3359c32 100644 --- a/.codespellrc +++ b/.codespellrc @@ -1,4 +1,4 @@ [codespell] -skip = .git,*.pdf,*.svg +skip = .git,*.pdf,*.svg,*.js,_build,*.html,*.rtf,External # -# ignore-words-list = +ignore-words-list = ons,ans,fpr,ttests,myu,whos,ser,htmp,fwe,dout From 35bf59aa5746e55eed09ff651d8a8b7707bb3126 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 28 Nov 2023 15:43:27 -0500 Subject: [PATCH 4/9] Consensus typo --- CanlabCore/@fmri_data/predict.m | 2 +- CanlabCore/mlpcr/mlpcr2.m | 12 ++++++------ CanlabCore/mlpcr/mlpcr3.m | 12 ++++++------ 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/CanlabCore/@fmri_data/predict.m b/CanlabCore/@fmri_data/predict.m index b271f5b5..79d598cc 100644 --- a/CanlabCore/@fmri_data/predict.m +++ b/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 diff --git a/CanlabCore/mlpcr/mlpcr2.m b/CanlabCore/mlpcr/mlpcr2.m index 08ee6c01..045eeb27 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 :: % @@ -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. % % Output :: @@ -117,7 +117,7 @@ % (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. @@ -185,7 +185,7 @@ 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'); From e6d4b99cc22538400f24652de48adf1efbd242f2 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 28 Nov 2023 15:55:34 -0500 Subject: [PATCH 5/9] [DATALAD RUNCMD] sagittal typo === Do not change lines below === { "chain": [], "cmd": "git-sedi saggital sagittal", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- CanlabCore/@fmridisplay/addpoints.m | 4 +- CanlabCore/@fmridisplay/fmridisplay.m | 10 ++-- CanlabCore/@fmridisplay/montage.m | 16 +++--- CanlabCore/@fmridisplay/zoom_in_on_regions.m | 4 +- CanlabCore/@image_vector/display_slices.m | 24 ++++---- CanlabCore/@image_vector/slices.m | 6 +- CanlabCore/@statistic_image/multi_threshold.m | 2 +- .../cluster_nmdsfig.m | 4 +- CanlabCore/Data_extraction/readim2.m | 2 +- .../ROI_drawing_tools/draw_anatomical_roi.m | 4 +- .../draw_anatomical_roi_2008.m | 4 +- ...gression_multisubject_bootstrapweightmap.m | 2 +- .../canlab_results_fmridisplay.m | 52 +++++++++--------- .../cluster_orthviews_classes.m | 2 +- .../cluster_orthviews_montage.m | 2 +- .../cluster_orthviews_showcenters.m | 2 +- .../make_figure_into_orthviews.m | 2 +- .../Visualization_functions/roi_contour_map.m | 6 +- .../spm_orthviews_showposition.m | 6 +- .../tor_ihb_TalSpace.m | 8 +-- .../create_anatomical_underlay_2016.m | 4 +- .../insula_ribbon_partial_script.m | 2 +- .../_build/doctrees/misc_tools.doctree | Bin 4585121 -> 4585121 bytes .../_build/doctrees/moduleslist.doctree | Bin 6558854 -> 6558854 bytes .../_build/doctrees/oo_tools.doctree | Bin 1052718 -> 1052718 bytes .../SPHINX_DOCS/_build/html/misc_tools.html | 20 +++---- .../SPHINX_DOCS/_build/html/moduleslist.html | 46 ++++++++-------- .../SPHINX_DOCS/_build/html/oo_tools.html | 10 ++-- .../SPHINX_DOCS/_build/html/searchindex.js | 2 +- docs_sphinx_old/misc_tools.html | 20 +++---- docs_sphinx_old/moduleslist.html | 46 ++++++++-------- docs_sphinx_old/oo_tools.html | 10 ++-- docs_sphinx_old/searchindex.js | 2 +- 33 files changed, 162 insertions(+), 162 deletions(-) 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 089326cb..ba8e0e64 100644 --- a/CanlabCore/@fmridisplay/fmridisplay.m +++ b/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'); diff --git a/CanlabCore/@fmridisplay/montage.m b/CanlabCore/@fmridisplay/montage.m index d3bab7ba..33fc0af6 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_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/Visualization_functions/canlab_results_fmridisplay.m b/CanlabCore/Visualization_functions/canlab_results_fmridisplay.m index 036f07f9..e7bfdb57 100644 --- a/CanlabCore/Visualization_functions/canlab_results_fmridisplay.m +++ b/CanlabCore/Visualization_functions/canlab_results_fmridisplay.m @@ -51,9 +51,9 @@ % % **'montagetype':** % -% '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 +% '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 % '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 @@ -260,7 +260,7 @@ 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'); @@ -358,20 +358,20 @@ 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; @@ -427,15 +427,15 @@ 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 @@ -449,8 +449,8 @@ 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 @@ -483,8 +483,8 @@ 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 @@ -534,8 +534,8 @@ axh = axes('Position', [-0.02 .75-.3 .17 .17]); % [-0.02 0.15+shiftvals(i) .17 .17]); axh(2) = axes('Position', [.022 .854-.3 .17 .17]); - %o2 = montage(o2, 'saggital', 'wh_slice', [0 0 0], 'existing_axes', axh, 'noverbose'); - o2 = montage(o2, 'volume_data', dat, 'saggital', 'slice_range', [-2 2], 'spacing', 4, 'onerow', 'noverbose', 'existing_axes', axh); + %o2 = montage(o2, 'sagittal', 'wh_slice', [0 0 0], 'existing_axes', axh, 'noverbose'); + o2 = montage(o2, 'volume_data', dat, 'sagittal', 'slice_range', [-2 2], 'spacing', 4, 'onerow', 'noverbose', 'existing_axes', axh); %ss = get(0, 'ScreenSize'); %set(gcf, 'Position', [round(ss(3)/12) round(ss(4)*.9) round(ss(3)*.8) round(ss(4)/5.5) ]) % this line messes p the @@ -549,14 +549,14 @@ o2 = montage(o2, 'coronal', 'slice_range', [-40 50], 'onerow', 'spacing', 8, 'noverbose'); wh_montages = 1; - case 'saggital' - o2 = montage(o2, 'saggital', 'wh_slice', xyz, 'onerow', 'noverbose'); + case 'sagittal' + o2 = montage(o2, 'sagittal', 'wh_slice', xyz, 'onerow', 'noverbose'); wh_montages = 1; case 'allslices' - [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); axh = axes('Position', [-0.02 0.37 .17 .17]); @@ -569,8 +569,8 @@ 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); % coronal @@ -617,8 +617,8 @@ % 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 @@ -651,13 +651,13 @@ 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'); case 'compact2' [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/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/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/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/misc_tools.doctree b/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/misc_tools.doctree index 1f10a161eaee4735d52cb25cf27cbbfcba7455f7..2c002520fa09f794481b2b8d6548107156f68633 100644 GIT binary patch delta 549 zcmZ|LyDx)L7{~FvZ|hR`OY7RY-_@lkEqZ9NNQBL3?qKU8F^EL_C%lWG6N5;aiW7r@ z!D0|3L^?L2kqFVw<$Id289sTQ-+7<&=H!XK8+sI5r`q$O9t_FEp|)&MjWecMbs8fO z*S4vV>$nCTCYX_jd=#J%78IcvB`8H1%29zzRG}JH*ieI7)S(^?XoMXOG@%(SXhj>^ z(Sc5Mp&LEuMIZX%!~g~{gkiWaf>Dgg>$v;OWeSEu#@(xXMc%%+kF~#O5KkhTDL2M3 z0gv2Fc@sryC%%lg#n?!Duhe1)n8XyOr7z=KJK}@f+Z9im8mEcLo_%37sN>6X@o7`X zt_LwJlec0uw`Y>eSicwQpOSEpo4I%w4*8i9H)eHAvgWC)GS0F%8qtJiw4fDj zXh#P+(FF&((Su&}p&tVngcB|dVHhJa9(BiDIcw{i#_fxHS>8OmPqe>i5Kn{KDK|zj zhH<%_@+1n>PP`dUv$2)-T&cwnFo8)-NpHrxddvrTurD4pHBJ+ejzeMC)bZuH_^49H zu6yB>$s4hf-80E$Y}^U;Pf0k+&Ro2S2KkW^*CusLvYORZ8oTlSDIR`9FqsyZ#*9p+ teZARtmVNog)x^S=?^V@^=3k`By>Fi>`?7xq0=hq-&j$3lm_8rM`~b6G27Ukl diff --git a/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/moduleslist.doctree b/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/moduleslist.doctree index a84d2b742e246963c398482b6640ae099ebdcc0a..dc4c4a09235d3367c596e6cbf8be3ffaf5a2d7a2 100644 GIT binary patch delta 1022 zcmajeNlX(_7zgmQlvfG^mK|&>RIo@}5k`@!EEN^Og;uL}bf{9iNc12Hk#NFgWHfm2 zVn&RS8V{l|8iVE~s250#Mh+fa4#>eJB(*Vy8^(bCzX=#G>fx97ZSQ5~b=rUXQc^#h zQVfbwNm5Ko@#FPl1JkJ%$yd!MjrYDAy1h9WAo&#_$1`jH8I{5^A;{w$?yDIeI(VufR<)wYne z(E4hgg$?6%a<>hM_J{-thL zd%PA%g*4vd6+R7OlD9n*o*QWk0y}SfArvoWHm&caaC)I-@81hKjYxs?Zo+C=%EU`(QsG z62rHKY05bje!#y^hFx^;99gseO+_-KLaxk)-{n#nnX3PG2r9L_Olh39Qo_@+q!Tow zb%~Ol50*(2`Zud*XT8$wV&>4UR!MI#sGHoO@45}l38QS=WKa#jcJ7ZIkfQ5pY=}3MGETc$OmWqntLaS9fI#ekhkmx}YBjJS0$Y}83 z#f%Um7!RT`8iVE~s250#Mh+fa4#>eJB(*Vy8^(bCzX>&7)Wa|D+uqB}>$LCo<%B*s ztr!%elAt6iNe|iA3S&nn|5m|D3F&rWkSt#+6B?O*CP zwcBlm6iDUWZsF4aCVA^K;kl8vAh7X<7eY}yvueFBg)@sSE4NPyik)`cj0(r-UR6s> zfHX*lC18OJ$b>A&h8)O+JjjOvSPE9KfgP4XArwI|EQb;(g%#j{GFS=a-~<=AVHH%s zYVbfMh_D9MLKUooYVg8(*Z>=$25O-W>cIz_paC|+7T5}nunn4^8Mea?*a^G1CDwAs zo6ymDQnQr$13azNf7kFk)sWs(#~gkLz;4*X#~i_*DRi|%Vz5Y?stk_Pg(88yun+e0 zAu)7ogrF7M2#)7Pc+yIe(clOQz@jW!DDLv;VT2gXk-N*_UAvZ-4ZU z9f&!$Kl;b{@D)fw<2x?t?GIjZl{3M4C2zQ;i{50Ag)IkN^Mx delta 168 zcmZ3tz+v42hlUo$7N!>F7M2#)7Pc+yIe(ebGpFbMW!DDLv;VT2gXk-N*_UAvZ-4ZU z9f&!$Kl;b{@D)fw<2x?t?GIjZl{3M4C2zQ;i{504!%g^Z)<= 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..7ff983bb 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 Toolsto plot montage of slices to the screen

sagg:
-

to rotate to saggital view

+

to rotate to sagittal view

cor:

to rotate to coronal view

@@ -17002,7 +17002,7 @@

Visualization_functions 
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);
@@ -18429,7 +18429,7 @@ 
Visualization_functions

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

@@ -19928,7 +19928,7 @@

Visualization_functions
Visualization_functions.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.

 @@ -19984,7 +19984,7 @@

Visualization_functions
‘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’:
@@ -20017,7 +20017,7 @@

Visualization_functions
  • [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
@@ -21085,12 +21085,12 @@

Visualization_functions
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

@@ -2962,7 +2962,7 @@

Object Oriented ToolsSolid 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
    • @@ -2999,7 +2999,7 @@

    Object Oriented Tools{‘close’, ‘closeenough’, ‘close_enough’}:

    close_enough = varargin{i+1};

    -
    {‘sagg’,’saggital’,’sagittal’}:
    +
    {‘sagg’,’sagittal’,’sagittal’}:

    orientation = ‘sagittal’;

    {‘MarkerSize’, ‘markersize’}:
    @@ -3038,7 +3038,7 @@

    Object Oriented Toolsfollowed 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
    @@ -3076,15 +3076,15 @@

    Object Oriented Tools

    Define new axes in existing figure, and use those for montage:

    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, @@ -3819,9 +3819,9 @@

    fmridisplay_helper_functions
    fastmontage(dat);
 fastmontage(dat, 'coronal');
-fastmontage(dat, 'saggital', 'spacing', 10);
-fastmontage(dat, 'saggital', 'spacing', 10, 'vertical');
-fastmontage(dat, 'saggital', 'slices_per_row', 12);
+fastmontage(dat, 'sagittal', 'spacing', 10);
+fastmontage(dat, 'sagittal', 'spacing', 10, 'vertical');
+fastmontage(dat, 'sagittal', 'slices_per_row', 12);
    @@ -5011,7 +5011,7 @@

    fmridisplay_helper_functions

    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

    @@ -5058,7 +5058,7 @@

    fmridisplay_helper_functionsto plot montage of slices to the screen

    sagg:
    -

    to rotate to saggital view

    +

    to rotate to sagittal view

    cor:

    to rotate to coronal view

    @@ -26906,7 +26906,7 @@

    Visualization_functions 
    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);
@@ -28333,7 +28333,7 @@ 
    Visualization_functions

    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

    @@ -29832,7 +29832,7 @@

    Visualization_functions
    Visualization_functions.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.

     @@ -29888,7 +29888,7 @@

    Visualization_functions
    ‘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’:
    @@ -29921,7 +29921,7 @@

    Visualization_functions
    • [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
    @@ -30989,12 +30989,12 @@

    Visualization_functions
    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
    @@ -4098,7 +4098,7 @@

    fmridisplay

    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

    @@ -4145,7 +4145,7 @@

    fmridisplayMiscellaneous Toolsto plot montage of slices to the screen

    sagg:
    -

    to rotate to saggital view

    +

    to rotate to sagittal view

    cor:

    to rotate to coronal view

    @@ -17002,7 +17002,7 @@

    Visualization_functions 
    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);
@@ -18429,7 +18429,7 @@ 
    Visualization_functions

    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

    @@ -19928,7 +19928,7 @@

    Visualization_functions
    Visualization_functions.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.

     @@ -19984,7 +19984,7 @@

    Visualization_functions
    ‘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’:
    @@ -20017,7 +20017,7 @@

    Visualization_functions
    • [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
    @@ -21085,12 +21085,12 @@

    Visualization_functions
    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

    @@ -2962,7 +2962,7 @@

    Object Oriented ToolsSolid 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
    • @@ -2999,7 +2999,7 @@

    Object Oriented Tools{‘close’, ‘closeenough’, ‘close_enough’}:

    close_enough = varargin{i+1};

    -
    {‘sagg’,’saggital’,’sagittal’}:
    +
    {‘sagg’,’sagittal’,’sagittal’}:

    orientation = ‘sagittal’;

    {‘MarkerSize’, ‘markersize’}:
    @@ -3038,7 +3038,7 @@

    Object Oriented Toolsfollowed 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
    @@ -3076,15 +3076,15 @@

    Object Oriented Tools

    Define new axes in existing figure, and use those for montage:

    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, @@ -3819,9 +3819,9 @@

    fmridisplay_helper_functions
    fastmontage(dat);
 fastmontage(dat, 'coronal');
-fastmontage(dat, 'saggital', 'spacing', 10);
-fastmontage(dat, 'saggital', 'spacing', 10, 'vertical');
-fastmontage(dat, 'saggital', 'slices_per_row', 12);
+fastmontage(dat, 'sagittal', 'spacing', 10);
+fastmontage(dat, 'sagittal', 'spacing', 10, 'vertical');
+fastmontage(dat, 'sagittal', 'slices_per_row', 12);
    @@ -5011,7 +5011,7 @@

    fmridisplay_helper_functions

    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

    @@ -5058,7 +5058,7 @@

    fmridisplay_helper_functionsto plot montage of slices to the screen

    sagg:
    -

    to rotate to saggital view

    +

    to rotate to sagittal view

    cor:

    to rotate to coronal view

    @@ -26906,7 +26906,7 @@

    Visualization_functions 
    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);
@@ -28333,7 +28333,7 @@ 
    Visualization_functions

    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

    @@ -29832,7 +29832,7 @@

    Visualization_functions
    Visualization_functions.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.

     @@ -29888,7 +29888,7 @@

    Visualization_functions
    ‘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’:
    @@ -29921,7 +29921,7 @@

    Visualization_functions
    • [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
    @@ -30989,12 +30989,12 @@

    Visualization_functions
    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
    @@ -4098,7 +4098,7 @@

    fmridisplay

    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

    @@ -4145,7 +4145,7 @@

    fmridisplay Date: Tue, 28 Nov 2023 15:56:01 -0500 Subject: [PATCH 6/9] [DATALAD RUNCMD] boostrap typo === Do not change lines below === { "chain": [], "cmd": "git-sedi boostrap bootstrap", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- CanlabCore/@fmri_data/predict.m | 2 +- .../xval_bestsubsets_brain.m | 2 +- .../xval_lasso_brain.m | 2 +- .../xval_lasso_brain_featureselect.m | 2 +- .../xval_ridge_brain.m | 2 +- .../Statistics_tools/canlab_run_paired_SVM.m | 2 +- .../scn_stats_helper_functions.m | 2 +- .../Visualization_functions/conf_region.m | 2 +- .../_build/doctrees/fmridata.doctree | Bin 211662 -> 211665 bytes .../_build/doctrees/misc_tools.doctree | Bin 4585121 -> 4585123 bytes .../_build/doctrees/moduleslist.doctree | Bin 6558854 -> 6558858 bytes .../_build/doctrees/oo_tools.doctree | Bin 1052718 -> 1052720 bytes .../SPHINX_DOCS/_build/html/fmridata.html | 2 +- .../SPHINX_DOCS/_build/html/misc_tools.html | 2 +- .../SPHINX_DOCS/_build/html/moduleslist.html | 2 +- .../SPHINX_DOCS/_build/html/searchindex.js | 2 +- docs_sphinx_old/fmridata.html | 2 +- docs_sphinx_old/misc_tools.html | 2 +- docs_sphinx_old/moduleslist.html | 2 +- docs_sphinx_old/searchindex.js | 2 +- 20 files changed, 16 insertions(+), 16 deletions(-) diff --git a/CanlabCore/@fmri_data/predict.m b/CanlabCore/@fmri_data/predict.m index 79d598cc..39dd2392 100644 --- a/CanlabCore/@fmri_data/predict.m +++ b/CanlabCore/@fmri_data/predict.m @@ -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/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_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/scn_stats_helper_functions.m b/CanlabCore/Statistics_tools/scn_stats_helper_functions.m index 46984fac..e032d410 100644 --- a/CanlabCore/Statistics_tools/scn_stats_helper_functions.m +++ b/CanlabCore/Statistics_tools/scn_stats_helper_functions.m @@ -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/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/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/fmridata.doctree b/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/fmridata.doctree index eec16f135e86dfe9a7d45e04dad53090f16143e2..6a2cb3c0463ee0a4bee75e5a26eba510dccfd551 100644 GIT binary patch delta 39 scmX^2mFMDDo`x-qd?kz}+kwO;CLn#FjByJiV@Z2S1>^RT3Z|$-07iljegFUf delta 33 pcmcckmFL`7o`x-qd?nlYOBgpXZ9i1TxP`I3yn=Cic?DC{Aprli4k!Qs diff --git a/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/misc_tools.doctree b/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/misc_tools.doctree index 2c002520fa09f794481b2b8d6548107156f68633..eb805daa7c08940aae1bcb8a664478a3c50b9d85 100644 GIT binary patch delta 198 zcmWN^Npb;U7=YpG7DGY^f)GT^TFgVoJmws3VAZ9!7H^dUq}0DwuAr(flx^LkFcG4>5+hE6HCmM| vp8-QgZ}t4pE}DA!d>`svcaw^-n24#EiMd#arC5oz*odvziT&rI9csrv0iQ|e diff --git a/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/moduleslist.doctree b/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/moduleslist.doctree index dc4c4a09235d3367c596e6cbf8be3ffaf5a2d7a2..fcb4bb505ca1498e49e8d0564d0658db77c2b32f 100644 GIT binary patch delta 444 zcmWO2w@zCD06ekQn#|HU=b*jQ#=q zKb+wVcfE@3lUaW8n?FREW1a;TSz?(L2V>EtApV$2$1amYZ?T8KNWm&=th2!; 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    -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 7ff983bb..fcc3e36f 100644 --- a/docs_sphinx_old/SPHINX_DOCS/_build/html/misc_tools.html +++ b/docs_sphinx_old/SPHINX_DOCS/_build/html/misc_tools.html @@ -17604,7 +17604,7 @@

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    -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/misc_tools.html b/docs_sphinx_old/misc_tools.html index 7ff983bb..fcc3e36f 100644 --- a/docs_sphinx_old/misc_tools.html +++ b/docs_sphinx_old/misc_tools.html @@ -17604,7 +17604,7 @@

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documentation home","Object Oriented Tools","Toolboxes"],titleterms:{"new":[],aspectlib:[],canlab_canonical_brain:[],canlab_dataset:1,canlabcor:0,cluster_contig_region_tool:1,configur:[],content:[],data_extract:1,data_processing_tool:1,diagnost:[1,2],document:0,filename_tool:1,fmri_data:1,fmri_mask_imag:1,fmri_model:1,fmri_timeseri:[],fmridisplai:1,fmridisplay_helper_funct:1,glm_batch_tool:[1,2],hewma_util:1,home:0,hrf_est_toolbox2:[1,2],image_computation_tool:1,image_space_tool:1,image_threshold:1,image_vector:1,index_image_manip_tool:1,indic:0,instal:[],manual:[],misc_util:1,miscellan:1,model_building_tool:1,object:1,optimizedesign11:[1,2],orient:1,parcellation_tool:1,peak_coordin:1,python:[],region:1,roi_drawing_tool:1,statistic_imag:1,statistics_tool:1,tabl:0,test:[],thi:[],titl:[],tool:1,toolbox:[1,2],usag:[],visualization_funct:1,wager_jneuro2011_placebo_mask:[],welcom:[]}}) \ No newline at end of file From aa2a34b44f1577bb206e7905973bfc923913cff0 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 28 Nov 2023 15:56:54 -0500 Subject: [PATCH 7/9] [DATALAD RUNCMD] Boostrap typo === Do not change lines below === { "chain": [], "cmd": "git-sedi Boostrap Bootstrap", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- CanlabCore/Statistics_tools/roc_plot.m | 2 +- .../scn_stats_helper_functions.m | 2 +- .../test_pattern_on_kragel_2018_n270_data.m | 2 +- .../_build/doctrees/misc_tools.doctree | Bin 4585123 -> 4585127 bytes .../_build/doctrees/moduleslist.doctree | Bin 6558858 -> 6558862 bytes .../SPHINX_DOCS/_build/html/misc_tools.html | 2 +- .../SPHINX_DOCS/_build/html/moduleslist.html | 2 +- docs_sphinx_old/misc_tools.html | 2 +- docs_sphinx_old/moduleslist.html | 2 +- 9 files changed, 7 insertions(+), 7 deletions(-) diff --git a/CanlabCore/Statistics_tools/roc_plot.m b/CanlabCore/Statistics_tools/roc_plot.m index 08a2001f..4d0cc090 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 e032d410..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 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/misc_tools.doctree b/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/misc_tools.doctree index eb805daa7c08940aae1bcb8a664478a3c50b9d85..d8a79e8c840043e082e22d05508916226a711936 100644 GIT binary patch delta 234 zcmWN?IZgs$0EXer2#9PhAcBH|g9^X0gR-~*av1w*Nv3!c6Ei&ru;2nD)6QM2xdUJE z#8@NFItez|B*_-rq)4;FE*bX7vd;mB z0ES`4SfjD`-h1r5Mx8(Q-n-F-xQGND5C;SoF9*u@gO`owy!bdVGq>@HD8TiR0ivZc=kV_u<6i`SJ#gtG=8Rb+^Nfp)9P)i;4 zG|)&B&9u-;8|`$^NsunO>7kcC`Wax5A%+=YlrhGcV3H}O2{FSgbJ$-d5w#pI5j6q7 z-??}0BC*)b?REUuH9_z1!Tea36aRiRPnPpyyGFx0uM4`UOS-Hpx~glst{b|kTe__~ ex~qG-uLpXlM|!L$da7r7t`{27OV4(%!XN()LUjTF delta 292 zcmWN=$4&xa0EN-WU<1cC3ijRsd++TZ#|Bstds(wKl9;&o5)&83ory1??v3*fK9%<* z=k@!|deJ8e2w)MUkRpmHp_C9|%CIS?f=a5W#-WB7~@PZ$rRJfFv}eCEU?HD%dD`<8tXsiGv|Nhj2-fS?~N09 z|9dcx&tBfBs~hU+rf%uB?&z*2HKl3Y(|tYALp{=C&FG0{^;FOFTrc!euk>1P^w#(C HckahOY^H2& 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 fcc3e36f..58c4e938 100644 --- a/docs_sphinx_old/SPHINX_DOCS/_build/html/misc_tools.html +++ b/docs_sphinx_old/SPHINX_DOCS/_build/html/misc_tools.html @@ -13668,7 +13668,7 @@

    Statistics_toolsBoostrapping of GLS

    +

    Bootstrapping of GLS

    ‘signperm’:

    Sign permutation test for intercept of GLS

    diff --git a/docs_sphinx_old/SPHINX_DOCS/_build/html/moduleslist.html b/docs_sphinx_old/SPHINX_DOCS/_build/html/moduleslist.html index a1f8e689..0c32077c 100644 --- a/docs_sphinx_old/SPHINX_DOCS/_build/html/moduleslist.html +++ b/docs_sphinx_old/SPHINX_DOCS/_build/html/moduleslist.html @@ -23572,7 +23572,7 @@

    Statistics_toolsBoostrapping of GLS

    +

    Bootstrapping of GLS

    ‘signperm’:

    Sign permutation test for intercept of GLS

    diff --git a/docs_sphinx_old/misc_tools.html b/docs_sphinx_old/misc_tools.html index fcc3e36f..58c4e938 100644 --- a/docs_sphinx_old/misc_tools.html +++ b/docs_sphinx_old/misc_tools.html @@ -13668,7 +13668,7 @@

    Statistics_toolsBoostrapping of GLS

    +

    Bootstrapping of GLS

    ‘signperm’:

    Sign permutation test for intercept of GLS

    diff --git a/docs_sphinx_old/moduleslist.html b/docs_sphinx_old/moduleslist.html index a1f8e689..0c32077c 100644 --- a/docs_sphinx_old/moduleslist.html +++ b/docs_sphinx_old/moduleslist.html @@ -23572,7 +23572,7 @@

    Statistics_toolsBoostrapping of GLS

    +

    Bootstrapping of GLS

    ‘signperm’:

    Sign permutation test for intercept of GLS

    From 85c1828d1030a0970e8e1bc0a03baeb42df2888e Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 28 Nov 2023 16:00:13 -0500 Subject: [PATCH 8/9] [DATALAD RUNCMD] decription typo === Do not change lines below === { "chain": [], "cmd": "git-sedi decription description", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- .../Visualization_functions/riverplot/riverplot_draw_layer.m | 2 +- .../Visualization_functions/riverplot/riverplot_draw_ribbon.m | 2 +- .../Visualization_functions/riverplot/riverplot_layer_names.m | 2 +- CanlabCore/Visualization_functions/riverplot/riverplot_ribbon.m | 2 +- .../Visualization_functions/riverplot/riverplot_ribbon_matrix.m | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) 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. From 02aa46c051ed3017f3abb0159521a509e1f2df54 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 28 Nov 2023 16:00:41 -0500 Subject: [PATCH 9/9] [DATALAD RUNCMD] indepenent typo === Do not change lines below === { "chain": [], "cmd": "git-sedi indepenent independent", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- CanlabCore/diagnostics/displayme.m | 2 +- .../_build/doctrees/moduleslist.doctree | Bin 6558862 -> 6558864 bytes .../_build/doctrees/toolboxes.doctree | Bin 585483 -> 585485 bytes .../SPHINX_DOCS/_build/html/moduleslist.html | 2 +- .../SPHINX_DOCS/_build/html/toolboxes.html | 2 +- docs_sphinx_old/moduleslist.html | 2 +- docs_sphinx_old/toolboxes.html | 2 +- 7 files changed, 5 insertions(+), 5 deletions(-) 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/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/moduleslist.doctree b/docs_sphinx_old/SPHINX_DOCS/_build/doctrees/moduleslist.doctree index 4323597bee8299a8c46efcd90272802f20fb4537..c64a012bca2a19678f0532ff15aa8c0c90ee252f 100644 GIT binary patch delta 388 zcmWm6M@|9(07l^qBZ`VRj5=0qU_~ro?;XVsDk_4Ca}MI-Pu!W=c?R|*T#N(wTzq-E z_fz#u4_`9mlc^^8)vOi;)T%bME2s{I)G140+3HfadTLI?GTeH@a!Q8b{?fVcitV5m zedxyk1~G&PhB1OsjA0y6#4v$LOko-`m_;1_?*!(tfJH1Ji4>Nxf>o?x9UIuh7Phg2 zUF=~W2ROtLj&Xuhq;ZCGWN?8?T;UowxWyf^$l)Fjctjpgc*Y9~ctsHd(0Eh8YDUrBcT$Fh%q)^H{&l(MhMCC#5;(ty%r=4f8cTO+H-e>XqmS5|u z<@$gvhn#Y$LvDH0DX+TJEuVViSFieHC?He)8qnak^<%Vu4Xf(-q{~g)v@nEWj39^* zMlptQOkfgIn8pldF^739AdCnWv4sD36f1}!j#aE-9SJ0{ffUl%#1^)(gI(-l9|t(Z z5sqVm?vY(bT2PPo$XGZj2w)NDeXWG5HkTWGZ3=?F)I+W0Wte_FE5UR FO8`k?60QIM delta 56 zcmeCZr`&x{xnT>VnCEmKFGij1&Yp}MjO{=s5HkTWGZ3=?F)I+W0Wte_A1{uBO8^p5 B5%&N9 diff --git a/docs_sphinx_old/SPHINX_DOCS/_build/html/moduleslist.html b/docs_sphinx_old/SPHINX_DOCS/_build/html/moduleslist.html index 0c32077c..55bc44cb 100644 --- a/docs_sphinx_old/SPHINX_DOCS/_build/html/moduleslist.html +++ b/docs_sphinx_old/SPHINX_DOCS/_build/html/moduleslist.html @@ -7277,7 +7277,7 @@

    Cluster_contig_region_tools diagnostics.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.

    diff --git a/docs_sphinx_old/SPHINX_DOCS/_build/html/toolboxes.html b/docs_sphinx_old/SPHINX_DOCS/_build/html/toolboxes.html index 574a6637..c7576cd4 100644 --- a/docs_sphinx_old/SPHINX_DOCS/_build/html/toolboxes.html +++ b/docs_sphinx_old/SPHINX_DOCS/_build/html/toolboxes.html @@ -616,7 +616,7 @@

    Toolboxes diagnostics.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.

    diff --git a/docs_sphinx_old/moduleslist.html b/docs_sphinx_old/moduleslist.html index 0c32077c..55bc44cb 100644 --- a/docs_sphinx_old/moduleslist.html +++ b/docs_sphinx_old/moduleslist.html @@ -7277,7 +7277,7 @@

    Cluster_contig_region_tools diagnostics.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.

    diff --git a/docs_sphinx_old/toolboxes.html b/docs_sphinx_old/toolboxes.html index 574a6637..c7576cd4 100644 --- a/docs_sphinx_old/toolboxes.html +++ b/docs_sphinx_old/toolboxes.html @@ -616,7 +616,7 @@

    Toolboxes diagnostics.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.