build based on 990f333

.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.6.7","generation_timestamp":"2024-10-15T21:01:04","documenter_version":"1.7.0"}}
+{"documenter":{"julia_version":"1.6.7","generation_timestamp":"2024-10-16T13:20:22","documenter_version":"1.7.0"}}

index.html

@@ -91,4 +91,4 @@
 
 resize_to_layout!(fig)
 
-save(&quot;mni_icbm152_gm.png&quot;, fig, px_per_unit = 1) </code></pre><p>Will produce <img src="https://github.com/vfonov/Minc2.jl/blob/main/docs/src/assets/mni_icbm152_gm.png?raw=true" alt="MNI-ICBM152"/></p><h2 id="More-examples"><a class="docs-heading-anchor" href="#More-examples">More examples</a><a id="More-examples-1"></a><a class="docs-heading-anchor-permalink" href="#More-examples" title="Permalink"></a></h2><p>See <code>examples</code> directory for more examples:</p><ul><li><code>bloor.jl</code> - Apply Blooring kernel to minc volume, equivalent to mincbloor</li><li><code>copy.jl</code> - Create a minc volume with the same dimensions as another one, copy voxels</li><li><code>draw_heatmap.jl</code> - Show MNI-ICBM152 template contours with GM proability map, as above</li><li><code>draw_seg.jl</code> - Show MNI-ICBM152 template contours with tissue masks overlays, as above</li><li><code>list_meta.jl</code> - List all metadata stored with minc file, similar to <code>mincheader</code></li><li><code>mriview_dual.jl</code> - Show two minc volumes side-by-side, interactively</li><li><code>mriview.jl</code> -  Show minc volume, interactively</li><li><code>multilabel_overlap.jl</code> - calculate voxel-wise generalized overlap coeffecient , method from http://dx.doi.org/10.1109/TMI.2006.880587</li><li><code>resample_grid.jl</code> - apply transformation to _grid file</li><li><code>resample_itk.jl</code> - resample nifti file with transformations produces by ANTS (multiple transformations can be applied in one go), equivalent to <code>antsApplyTransforms</code></li><li><code>resample.jl</code>  - apply transformation to minc volume, equivalent to <code>mincresample</code></li><li><code>xfm_to_jacobian.jl</code> - calculate jacobian determinant field, for a given .xfm file</li><li><code>mincinfo.jl</code> -  show information about mincfile(s) and store it in csv file, equivalent to <code>mincinfo</code></li></ul><h2 id="Documentation-for-MINC"><a class="docs-heading-anchor" href="#Documentation-for-MINC">Documentation for MINC</a><a id="Documentation-for-MINC-1"></a><a class="docs-heading-anchor-permalink" href="#Documentation-for-MINC" title="Permalink"></a></h2><p>Documentations for underlying libminc and minc tools is available at https://en.wikibooks.org/wiki/MINC</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="high_level/">High level functions »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Tuesday 15 October 2024 21:01">Tuesday 15 October 2024</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+save(&quot;mni_icbm152_gm.png&quot;, fig, px_per_unit = 1) </code></pre><p>Will produce <img src="https://github.com/vfonov/Minc2.jl/blob/main/docs/src/assets/mni_icbm152_gm.png?raw=true" alt="MNI-ICBM152"/></p><h2 id="More-examples"><a class="docs-heading-anchor" href="#More-examples">More examples</a><a id="More-examples-1"></a><a class="docs-heading-anchor-permalink" href="#More-examples" title="Permalink"></a></h2><p>See <code>examples</code> directory for more examples:</p><ul><li><code>bloor.jl</code> - Apply Blooring kernel to minc volume, equivalent to mincbloor</li><li><code>copy.jl</code> - Create a minc volume with the same dimensions as another one, copy voxels</li><li><code>draw_heatmap.jl</code> - Show MNI-ICBM152 template contours with GM proability map, as above</li><li><code>draw_seg.jl</code> - Show MNI-ICBM152 template contours with tissue masks overlays, as above</li><li><code>list_meta.jl</code> - List all metadata stored with minc file, similar to <code>mincheader</code></li><li><code>mriview_dual.jl</code> - Show two minc volumes side-by-side, interactively</li><li><code>mriview.jl</code> -  Show minc volume, interactively</li><li><code>multilabel_overlap.jl</code> - calculate voxel-wise generalized overlap coeffecient , method from http://dx.doi.org/10.1109/TMI.2006.880587</li><li><code>resample_grid.jl</code> - apply transformation to _grid file</li><li><code>resample_itk.jl</code> - resample nifti file with transformations produces by ANTS (multiple transformations can be applied in one go), equivalent to <code>antsApplyTransforms</code></li><li><code>resample.jl</code>  - apply transformation to minc volume, equivalent to <code>mincresample</code></li><li><code>xfm_to_jacobian.jl</code> - calculate jacobian determinant field, for a given .xfm file</li><li><code>mincinfo.jl</code> -  show information about mincfile(s) and store it in csv file, equivalent to <code>mincinfo</code></li></ul><h2 id="Documentation-for-MINC"><a class="docs-heading-anchor" href="#Documentation-for-MINC">Documentation for MINC</a><a id="Documentation-for-MINC-1"></a><a class="docs-heading-anchor-permalink" href="#Documentation-for-MINC" title="Permalink"></a></h2><p>Documentations for underlying libminc and minc tools is available at https://en.wikibooks.org/wiki/MINC</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="high_level/">High level functions »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Wednesday 16 October 2024 13:20">Wednesday 16 October 2024</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

plotting/index.html

@@ -25,7 +25,7 @@
     cmap = :rainbow,
     levels = [20,30],
     show_colorbar = true,
-    nslices = 4)</code></pre><p>Draws a segmentation <code>seg</code> on top of <code>anat</code> in a grid layout <code>layout</code></p><ul><li><code>layout</code> is a grid layout</li><li><code>anat</code> is a Volume3D with anatomical image</li><li><code>seg</code> is a Volume3D with discrete segemntations</li><li><code>labels</code> is a dictionary of labels to show</li><li><code>cmap</code> is a color map to use</li><li><code>levels</code> is a list of levels of <code>anat</code> to use for contours</li><li><code>show_colorbar</code> is a boolean flag to show colorbar</li><li><code>nslices</code> is a number of slices to show</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/vfonov/Minc2.jl/blob/7f8dcefff970f41b5b8d81225b43a84f79d2158e/src/minc_makie.jl#L4-L25">source</a></section></article><h3 id="Show-MNI-ICBM152-template-contours-with-GM-proability-map"><a class="docs-heading-anchor" href="#Show-MNI-ICBM152-template-contours-with-GM-proability-map">Show MNI-ICBM152 template contours with GM proability map</a><a id="Show-MNI-ICBM152-template-contours-with-GM-proability-map-1"></a><a class="docs-heading-anchor-permalink" href="#Show-MNI-ICBM152-template-contours-with-GM-proability-map" title="Permalink"></a></h3><pre><code class="language-julia hljs">using CairoMakie
+    nslices = 4)</code></pre><p>Draws a segmentation <code>seg</code> on top of <code>anat</code> in a grid layout <code>layout</code></p><ul><li><code>layout</code> is a grid layout</li><li><code>anat</code> is a Volume3D with anatomical image</li><li><code>seg</code> is a Volume3D with discrete segemntations</li><li><code>labels</code> is a dictionary of labels to show</li><li><code>cmap</code> is a color map to use</li><li><code>levels</code> is a list of levels of <code>anat</code> to use for contours</li><li><code>show_colorbar</code> is a boolean flag to show colorbar</li><li><code>nslices</code> is a number of slices to show</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/vfonov/Minc2.jl/blob/990f333f0ecdfe64a577cc06f401d7a2c1bfb6a5/src/minc_makie.jl#L4-L25">source</a></section></article><h3 id="Show-MNI-ICBM152-template-contours-with-GM-proability-map"><a class="docs-heading-anchor" href="#Show-MNI-ICBM152-template-contours-with-GM-proability-map">Show MNI-ICBM152 template contours with GM proability map</a><a id="Show-MNI-ICBM152-template-contours-with-GM-proability-map-1"></a><a class="docs-heading-anchor-permalink" href="#Show-MNI-ICBM152-template-contours-with-GM-proability-map" title="Permalink"></a></h3><pre><code class="language-julia hljs">using CairoMakie
 using Minc2
 
 # read T1w scan
@@ -50,7 +50,7 @@
     cmap=:rainbow, levels=[20, 40],
     heat_limits=nothing, 
     show_colorbar=true,
-    nslices=4)</code></pre><p>Draws a heatmap of <code>heat</code> on top of <code>anat</code> in a grid layout <code>layout</code>.</p><ul><li><code>layout</code> is a grid layout</li><li><code>anat</code> is a Volume3D with anatomical image</li><li><code>heat</code> is a Volume3D with overlay heatmap</li><li><code>heat_limits</code> limits for the heatmap</li><li><code>cmap</code> is a color map to use</li><li><code>levels</code> is a list of levels of <code>anat</code> to use for contours</li><li><code>show_colorbar</code> is a boolean flag to show colorbar</li><li><code>nslices</code> is a number of slices to show</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/vfonov/Minc2.jl/blob/7f8dcefff970f41b5b8d81225b43a84f79d2158e/src/minc_makie.jl#L93-L111">source</a></section></article><h3 id="Show-two-tailed-t-statistics-on-DBM-style-analysis"><a class="docs-heading-anchor" href="#Show-two-tailed-t-statistics-on-DBM-style-analysis">Show two-tailed t-statistics on DBM style analysis</a><a id="Show-two-tailed-t-statistics-on-DBM-style-analysis-1"></a><a class="docs-heading-anchor-permalink" href="#Show-two-tailed-t-statistics-on-DBM-style-analysis" title="Permalink"></a></h3><pre><code class="language-julia hljs">using CairoMakie
+    nslices=4)</code></pre><p>Draws a heatmap of <code>heat</code> on top of <code>anat</code> in a grid layout <code>layout</code>.</p><ul><li><code>layout</code> is a grid layout</li><li><code>anat</code> is a Volume3D with anatomical image</li><li><code>heat</code> is a Volume3D with overlay heatmap</li><li><code>heat_limits</code> limits for the heatmap</li><li><code>cmap</code> is a color map to use</li><li><code>levels</code> is a list of levels of <code>anat</code> to use for contours</li><li><code>show_colorbar</code> is a boolean flag to show colorbar</li><li><code>nslices</code> is a number of slices to show</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/vfonov/Minc2.jl/blob/990f333f0ecdfe64a577cc06f401d7a2c1bfb6a5/src/minc_makie.jl#L93-L111">source</a></section></article><h3 id="Show-two-tailed-t-statistics-on-DBM-style-analysis"><a class="docs-heading-anchor" href="#Show-two-tailed-t-statistics-on-DBM-style-analysis">Show two-tailed t-statistics on DBM style analysis</a><a id="Show-two-tailed-t-statistics-on-DBM-style-analysis-1"></a><a class="docs-heading-anchor-permalink" href="#Show-two-tailed-t-statistics-on-DBM-style-analysis" title="Permalink"></a></h3><pre><code class="language-julia hljs">using CairoMakie
 using Minc2
 
 # read T1w scan and crop black area around ROI
@@ -97,4 +97,4 @@
     alpha=0.7,
     colorbar_label=&quot;&quot;,
     slices_gap=5,
-    colorbar_gap=10)</code></pre><p>Draws a two-sided (symmetric positive and negative) heatmap of <code>heat</code> on top of <code>anat</code> in a grid layout <code>layout</code>.</p><ul><li><code>layout</code> is a grid layout</li><li><code>anat</code> is a Volume3D with anatomical image</li><li><code>mask</code> is a Volume3D with ROI</li><li><code>heat</code> is a Volume3D with overlay heatmap, can be arbitrary sampling</li><li><code>heat_limits</code> limits for the heatmap</li><li><code>cmap_pos</code> is a color map to use for positive values, if nothing then don&#39;t show positive values</li><li><code>cmap_neg</code> is a color map to use for negative values, if nothing then don&#39;t show negative values</li><li><code>levels</code> is a list of levels of <code>anat</code> to use for contours</li><li><code>show_colorbar</code> is a boolean flag to show colorbar</li><li><code>colorbar_label</code> is a label for the colorbar</li><li><code>nslices</code> is a number of slices to show</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/vfonov/Minc2.jl/blob/7f8dcefff970f41b5b8d81225b43a84f79d2158e/src/minc_makie.jl#L169-L198">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../high_level/">« High level functions</a><a class="docs-footer-nextpage" href="../geo/">Gemetric transformation functions »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Tuesday 15 October 2024 21:01">Tuesday 15 October 2024</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+    colorbar_gap=10)</code></pre><p>Draws a two-sided (symmetric positive and negative) heatmap of <code>heat</code> on top of <code>anat</code> in a grid layout <code>layout</code>.</p><ul><li><code>layout</code> is a grid layout</li><li><code>anat</code> is a Volume3D with anatomical image</li><li><code>mask</code> is a Volume3D with ROI</li><li><code>heat</code> is a Volume3D with overlay heatmap, can be arbitrary sampling</li><li><code>heat_limits</code> limits for the heatmap</li><li><code>cmap_pos</code> is a color map to use for positive values, if nothing then don&#39;t show positive values</li><li><code>cmap_neg</code> is a color map to use for negative values, if nothing then don&#39;t show negative values</li><li><code>levels</code> is a list of levels of <code>anat</code> to use for contours</li><li><code>show_colorbar</code> is a boolean flag to show colorbar</li><li><code>colorbar_label</code> is a label for the colorbar</li><li><code>nslices</code> is a number of slices to show</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/vfonov/Minc2.jl/blob/990f333f0ecdfe64a577cc06f401d7a2c1bfb6a5/src/minc_makie.jl#L169-L198">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../high_level/">« High level functions</a><a class="docs-footer-nextpage" href="../geo/">Gemetric transformation functions »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Wednesday 16 October 2024 13:20">Wednesday 16 October 2024</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>