deploy: 3229797

b-heifets · Sep 14, 2024 · 22e44ca · 22e44ca
1 parent 29d511d
commit 22e44ca
Show file tree

Hide file tree

Showing 87 changed files with 2,453 additions and 1,331 deletions.
diff --git a/_images/FSLeyes_Ai14_image_in_CCFv3_30um_space.JPG b/_images/FSLeyes_Ai14_image_in_CCFv3_30um_space.JPG
diff --git a/_images/FSLeyes_atlas_warped_to_tissue_from_reg.JPG b/_images/FSLeyes_atlas_warped_to_tissue_from_reg.JPG
diff --git a/_images/FSLeyes_autofl_image_from_reg.JPG b/_images/FSLeyes_autofl_image_from_reg.JPG
diff --git a/_images/Ilastik_brain_mask_example.JPG b/_images/Ilastik_brain_mask_example.JPG
diff --git a/_images/Ilastik_c-Fos_example.JPG b/_images/Ilastik_c-Fos_example.JPG
diff --git a/_images/brain_model_layout.JPG b/_images/brain_model_layout.JPG
diff --git a/_images/brain_model_settings_1.JPG b/_images/brain_model_settings_1.JPG
diff --git a/_images/brain_model_settings_2.JPG b/_images/brain_model_settings_2.JPG
diff --git a/_images/sunburst_1_flourish.JPG b/_images/sunburst_1_flourish.JPG
diff --git a/_images/sunburst_2_plot_types.JPG b/_images/sunburst_2_plot_types.JPG
diff --git a/_images/sunburst_3_adding_data.JPG b/_images/sunburst_3_adding_data.JPG
diff --git a/_images/sunburst_4_RGB_values.JPG b/_images/sunburst_4_RGB_values.JPG
diff --git a/_modules/unravel/cluster_stats/brain_model.html b/_modules/unravel/cluster_stats/brain_model.html
@@ -461,18 +461,8 @@ <h1>Source code for unravel.cluster_stats.brain_model</h1><div class="highlight"
     <span class="n">final_data</span> <span class="o">=</span> <span class="n">img</span> <span class="o">*</span> <span class="n">atlas_img</span>
 
     <span class="c1"># Save the bilateral version of the cluster index with ABA colors</span>
-
     <span class="n">nib</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">nib</span><span class="o">.</span><span class="n">Nifti1Image</span><span class="p">(</span><span class="n">final_data</span><span class="p">,</span> <span class="n">atlas_nii</span><span class="o">.</span><span class="n">affine</span><span class="p">,</span> <span class="n">atlas_nii</span><span class="o">.</span><span class="n">header</span><span class="p">),</span> <span class="n">output</span><span class="p">)</span>
 
-    <span class="c1"># Calculate and save histogram</span>
-    <span class="n">histogram</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">histogram</span><span class="p">(</span><span class="n">final_data</span><span class="p">,</span> <span class="n">bins</span><span class="o">=</span><span class="mi">21144</span><span class="p">,</span> <span class="nb">range</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">21144</span><span class="p">))</span>
-
-    <span class="c1"># Exclude the background (region 0) from the histogram</span>
-    <span class="n">histogram</span> <span class="o">=</span> <span class="n">histogram</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
-
-    <span class="c1"># Determine what regions are present based on the histogram</span>
-    <span class="n">present_regions</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">histogram</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span>  <span class="c1"># Add 1 to account for the background</span>
-
     <span class="c1"># Get R, G, B values for each region</span>
     <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">csv_path</span> <span class="o">==</span> <span class="s1">&#39;CCFv3-2017_regional_summary.csv&#39;</span> <span class="ow">or</span> <span class="n">args</span><span class="o">.</span><span class="n">csv_path</span> <span class="o">==</span> <span class="s1">&#39;CCFv3-2020_regional_summary.csv&#39;</span><span class="p">:</span> 
         <span class="n">color_map</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">Path</span><span class="p">(</span><span class="vm">__file__</span><span class="p">)</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">parent</span> <span class="o">/</span> <span class="s1">&#39;core&#39;</span> <span class="o">/</span> <span class="s1">&#39;csvs&#39;</span> <span class="o">/</span> <span class="n">args</span><span class="o">.</span><span class="n">csv_path</span><span class="p">)</span> <span class="c1">#(Region_ID,ID_Path,Region,Abbr,General_Region,R,G,B)</span>
@@ -484,6 +474,7 @@ <h1>Source code for unravel.cluster_stats.brain_model</h1><div class="highlight"
         <span class="n">Path</span><span class="p">(</span><span class="n">txt_output</span><span class="p">)</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
 
     <span class="c1"># Determine the RGB color for bars based on the region_id</span>
+    <span class="n">present_regions</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">final_data</span><span class="p">[</span><span class="n">final_data</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">])</span>
     <span class="k">for</span> <span class="n">region_id</span> <span class="ow">in</span> <span class="n">present_regions</span><span class="p">:</span>
         <span class="n">combined_region_id</span> <span class="o">=</span> <span class="n">region_id</span> <span class="k">if</span> <span class="n">region_id</span> <span class="o">&lt;</span> <span class="mi">20000</span> <span class="k">else</span> <span class="n">region_id</span> <span class="o">-</span> <span class="mi">20000</span>
         <span class="n">region_rgb</span> <span class="o">=</span> <span class="n">color_map</span><span class="p">[</span><span class="n">color_map</span><span class="p">[</span><span class="s1">&#39;Region_ID&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="n">combined_region_id</span><span class="p">][[</span><span class="s1">&#39;R&#39;</span><span class="p">,</span> <span class="s1">&#39;G&#39;</span><span class="p">,</span> <span class="s1">&#39;B&#39;</span><span class="p">]]</span>

diff --git a/_modules/unravel/cluster_stats/fdr.html b/_modules/unravel/cluster_stats/fdr.html
@@ -377,6 +377,10 @@ <h1>Source code for unravel.cluster_stats.fdr</h1><div class="highlight"><pre>
 <span class="sd">    - The cluster index will be split accoding to the effect directions</span>
 <span class="sd">    - ``cstats_fdr`` -i vox_p_fstat1.nii.gz -mas mask.nii.gz -q 0.05 -a1 group1_avg.nii.gz -a2 group2_avg.nii.gz -o stats_info_g1_v_g2 -v</span>
 
+<span class="sd">Next commands:</span>
+<span class="sd">    - ``cstats_mirror_indices`` to mirror the cluster indices to the other hemisphere (if bilateral data processed with a hemispheric mask).</span>
+<span class="sd">    - ``cstats_validation`` to validate the cluster indices (if unilateral data or bilateral data processed with a whole brain mask).</span>
+
 <span class="sd">Usage</span>
 <span class="sd">-----</span>
 <span class="sd">    cstats_fdr -i path/vox_p_tstat1.nii.gz -mas path/mask.nii.gz -q 0.05 0.01 0.001 [-ms 100] [-o output_dir] [-a1 path/avg_img1.nii.gz] [-a2 path/avg_img2.nii.gz] [-th 10] [-v]</span>

diff --git a/_modules/unravel/cluster_stats/fdr_range.html b/_modules/unravel/cluster_stats/fdr_range.html
@@ -357,6 +357,9 @@ <h1>Source code for unravel.cluster_stats.fdr_range</h1><div class="highlight"><
 <span class="sd">Inputs: </span>
 <span class="sd">    - p value map (e.g., *vox_p_*stat*.nii.gz from vstats)</span>
 
+<span class="sd">Next command:</span>
+<span class="sd">    - ``cstats_fdr`` to correct for multiple comparisons (use the q values from ``cstats_fdr_range``).</span>
+
 <span class="sd">Usage:</span>
 <span class="sd">------</span>
 <span class="sd">    cstats_fdr_range -i path/vox_p_tstat1.nii.gz -mas path/mask.nii.gz [-q 0.00001 0.00005 0.0001 0.0005 0.001 0.005 0.01 0.05 0.1 0.15 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 0.95 0.99 0.999 0.9999] [-th 22] [-v]</span>

diff --git a/_modules/unravel/cluster_stats/mean_IF.html b/_modules/unravel/cluster_stats/mean_IF.html
@@ -355,8 +355,8 @@ <h1>Source code for unravel.cluster_stats.mean_IF</h1><div class="highlight"><pr
 <span class="sd">Use ``cstats_mean_IF`` from UNRAVEL to measure mean intensity of immunofluorescence staining in clusters.</span>
 
 <span class="sd">Prereqs: </span>
-<span class="sd">    - vstats</span>
-<span class="sd">    - cstats_fdr</span>
+<span class="sd">    - ``vstats``</span>
+<span class="sd">    - ``cstats_fdr``</span>
 
 <span class="sd">Inputs:</span>
 <span class="sd">    - This can be run from the vstats directory (will process .nii.gz images in the current directory)</span>
@@ -367,10 +367,10 @@ <h1>Source code for unravel.cluster_stats.mean_IF</h1><div class="highlight"><pr
 
 <span class="sd">Next steps:</span>
 <span class="sd">    - cd cluster_mean_IF...</span>
-<span class="sd">    - utils_prepend -sk &lt;path/sample_key.csv&gt; -f  # If needed</span>
+<span class="sd">    - ``utils_prepend`` -sk &lt;path/sample_key.csv&gt; -f  # If needed</span>
 <span class="sd">    - [``cstats_index`` and ``cstats_table``]  # for an xlsx table and anatomically ordered clusters that can be used with ``cstats_prism``</span>
-<span class="sd">    - cstats_mean_IF_summary --order Control Treatment --labels Control Treatment -t ttest  # Plots each cluster and outputs a summary table w/ stats</span>
-<span class="sd">    - cstats_mean_IF_summary --order group3 group2 group1 --labels Group_3 Group_2 Group_1  # Tukey tests</span>
+<span class="sd">    - ``cstats_mean_IF_summary`` --order Control Treatment --labels Control Treatment -t ttest  # Plots each cluster and outputs a summary table w/ stats</span>
+<span class="sd">    - ``cstats_mean_IF_summary`` --order group3 group2 group1 --labels Group_3 Group_2 Group_1  # Tukey tests</span>
 
 <span class="sd">Usage:</span>
 <span class="sd">------</span>