🎨 Update logos fix (#299)

FCP-INDI · Feb 28, 2023 · 341af9b · 341af9b
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diff --git a/404.html b/404.html
@@ -20,7 +20,7 @@
 <body>
   <section id="header">
     <div class="inner">
-      <span><img src="https://fcp-indi.github.io/images/CPAC-CMI.png" width="100%" height="100%" alt="Configurable Pipeline for the Analysis of Connectomes - Child Mind Institute C-PAC"/></span>
+      <span><img src="https://fcp-indi.github.io/images/cpac_logo.svg" width="100%" height="100%" alt="Configurable Pipeline for the Analysis of Connectomes - Child Mind Institute C-PAC"/></span>
 
       <p>Configurable Pipeline for the Analysis of Connectomes</p>
 

diff --git a/docs/nightly/.buildinfo b/docs/nightly/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 9c836cd64f07c447e228d6e1f6ba8035
+config: e5f22e0bd77e2090f27d9757d0fa7120
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/nightly/_modules/CPAC/cwas/cwas.html b/docs/nightly/_modules/CPAC/cwas/cwas.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/cwas/pipeline.html b/docs/nightly/_modules/CPAC/cwas/pipeline.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/easy_thresh/easy_thresh.html b/docs/nightly/_modules/CPAC/easy_thresh/easy_thresh.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/func_preproc/func_preproc.html b/docs/nightly/_modules/CPAC/func_preproc/func_preproc.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/generate_motion_statistics/generate_motion_statistics.html b/docs/nightly/_modules/CPAC/generate_motion_statistics/generate_motion_statistics.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/group_analysis/group_analysis.html b/docs/nightly/_modules/CPAC/group_analysis/group_analysis.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/network_centrality/utils.html b/docs/nightly/_modules/CPAC/network_centrality/utils.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/nuisance/bandpass.html b/docs/nightly/_modules/CPAC/nuisance/bandpass.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/nuisance/nuisance.html b/docs/nightly/_modules/CPAC/nuisance/nuisance.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/nuisance/utils.html b/docs/nightly/_modules/CPAC/nuisance/utils.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/nuisance/utils/compcor.html b/docs/nightly/_modules/CPAC/nuisance/utils/compcor.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/pipeline/nipype_pipeline_engine/engine.html b/docs/nightly/_modules/CPAC/pipeline/nipype_pipeline_engine/engine.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/pipeline/random_state/seed.html b/docs/nightly/_modules/CPAC/pipeline/random_state/seed.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/pipeline/schema.html b/docs/nightly/_modules/CPAC/pipeline/schema.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>
@@ -391,7 +391,7 @@ <h1>Source code for CPAC.pipeline.schema</h1><div class="highlight"><pre>
     <span class="s1">&#39;brain_extraction&#39;</span><span class="p">:</span> <span class="p">{</span>
         <span class="s1">&#39;using&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;3dSkullStrip&#39;</span><span class="p">,</span> <span class="s1">&#39;BET&#39;</span><span class="p">,</span> <span class="s1">&#39;UNet&#39;</span><span class="p">,</span> <span class="s1">&#39;niworkflows-ants&#39;</span><span class="p">,</span>
                   <span class="s1">&#39;FreeSurfer-BET-Tight&#39;</span><span class="p">,</span> <span class="s1">&#39;FreeSurfer-BET-Loose&#39;</span><span class="p">,</span>
-                  <span class="s1">&#39;FreeSurfer-ABCD&#39;</span><span class="p">]</span>
+                  <span class="s1">&#39;FreeSurfer-ABCD&#39;</span><span class="p">,</span> <span class="s1">&#39;FreeSurfer-Brainmask&#39;</span><span class="p">]</span>
     <span class="p">},</span>
     <span class="s1">&#39;centrality&#39;</span><span class="p">:</span> <span class="p">{</span>
        <span class="s1">&#39;method_options&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;degree_centrality&#39;</span><span class="p">,</span> <span class="s1">&#39;eigenvector_centrality&#39;</span><span class="p">,</span>
@@ -753,6 +753,7 @@ <h1>Source code for CPAC.pipeline.schema</h1><div class="highlight"><pre>
                 <span class="s1">&#39;BiasFieldSmoothingSigma&#39;</span><span class="p">:</span> <span class="n">Maybe</span><span class="p">(</span><span class="nb">int</span><span class="p">),</span>
             <span class="p">},),</span>
         <span class="p">),</span>
+
         <span class="s1">&#39;acpc_alignment&#39;</span><span class="p">:</span> <span class="n">Required</span><span class="p">(</span>
             <span class="c1"># require &#39;T1w_brain_ACPC_template&#39; and</span>
             <span class="c1"># &#39;T2w_brain_ACPC_template&#39; if &#39;acpc_target&#39; is &#39;brain&#39;</span>
@@ -1028,7 +1029,9 @@ <h1>Source code for CPAC.pipeline.schema</h1><div class="highlight"><pre>
     <span class="s1">&#39;surface_analysis&#39;</span><span class="p">:</span> <span class="p">{</span>
         <span class="s1">&#39;freesurfer&#39;</span><span class="p">:</span> <span class="p">{</span>
             <span class="s1">&#39;run_reconall&#39;</span><span class="p">:</span> <span class="n">bool1_1</span><span class="p">,</span>
-            <span class="s1">&#39;reconall_args&#39;</span><span class="p">:</span> <span class="n">Maybe</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span>
+            <span class="s1">&#39;reconall_args&#39;</span><span class="p">:</span> <span class="n">Maybe</span><span class="p">(</span><span class="nb">str</span><span class="p">),</span>
+            <span class="c1"># &#39;generate_masks&#39;: bool1_1,</span>
+            <span class="s1">&#39;ingress_reconall&#39;</span><span class="p">:</span> <span class="n">bool1_1</span><span class="p">,</span>
         <span class="p">},</span>
         <span class="s1">&#39;post_freesurfer&#39;</span><span class="p">:</span> <span class="p">{</span>
             <span class="s1">&#39;run&#39;</span><span class="p">:</span> <span class="n">bool1_1</span><span class="p">,</span>

diff --git a/docs/nightly/_modules/CPAC/qc/xcp.html b/docs/nightly/_modules/CPAC/qc/xcp.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/registration/registration.html b/docs/nightly/_modules/CPAC/registration/registration.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>
@@ -2526,7 +2526,9 @@ <h1>Source code for CPAC.registration.registration</h1><div class="highlight"><p
 <span class="sd">                  &quot;space-longitudinal_desc-brain_mask&quot;,</span>
 <span class="sd">                  &quot;space-T1w_desc-acpcbrain_mask&quot;],</span>
 <span class="sd">                 [&quot;desc-restore_T1w&quot;, &quot;desc-head_T1w&quot;, &quot;desc-preproc_T1w&quot;,</span>
-<span class="sd">                  &quot;space-longitudinal_desc-reorient_T1w&quot;]),</span>
+<span class="sd">                  &quot;space-longitudinal_desc-reorient_T1w&quot;],</span>
+<span class="sd">                 &quot;space-template_desc-head_T1w&quot;,</span>
+<span class="sd">                 &quot;space-template_desc-preproc_T1w&quot;),</span>
 <span class="sd">                &quot;T1w-template&quot;,</span>
 <span class="sd">                &quot;T1w-brain-template&quot;,</span>
 <span class="sd">                &quot;T1w-brain-template-mask&quot;,</span>
@@ -2829,7 +2831,8 @@ <h1>Source code for CPAC.registration.registration</h1><div class="highlight"><p
 <span class="sd">                 &quot;T1w-template&quot;,</span>
 <span class="sd">                 &quot;from-T1w_to-template_mode-image_xfm&quot;,</span>
 <span class="sd">                 &quot;from-template_to-T1w_mode-image_xfm&quot;,</span>
-<span class="sd">                 &quot;space-template_desc-brain_T1w&quot;)],</span>
+<span class="sd">                 &quot;space-template_desc-brain_T1w&quot;,</span>
+<span class="sd">                 &quot;space-template_desc-preproc_T1w&quot;)],</span>
 <span class="sd">     &quot;outputs&quot;: {&quot;space-template_desc-preproc_T1w&quot;: {</span>
 <span class="sd">                     &quot;Template&quot;: &quot;T1w-template&quot;},</span>
 <span class="sd">                 &quot;space-template_desc-head_T1w&quot;: {</span>
@@ -3696,7 +3699,8 @@ <h1>Source code for CPAC.registration.registration</h1><div class="highlight"><p
 <span class="sd">     &quot;option_key&quot;: &quot;None&quot;,</span>
 <span class="sd">     &quot;option_val&quot;: &quot;None&quot;,</span>
 <span class="sd">     &quot;inputs&quot;: [(&quot;desc-head_T1w&quot;,</span>
-<span class="sd">                 &quot;from-T1w_to-template_mode-image_xfm&quot;),</span>
+<span class="sd">                 &quot;from-T1w_to-template_mode-image_xfm&quot;,</span>
+<span class="sd">                 &quot;space-template_desc-head_T1w&quot;),</span>
 <span class="sd">                &quot;T1w-template&quot;],</span>
 <span class="sd">     &quot;outputs&quot;: {&quot;space-template_desc-head_T1w&quot;: {</span>
 <span class="sd">                     &quot;Template&quot;: &quot;T1w-template&quot;}}}</span>

diff --git a/docs/nightly/_modules/CPAC/reho/reho.html b/docs/nightly/_modules/CPAC/reho/reho.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/reho/utils.html b/docs/nightly/_modules/CPAC/reho/utils.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/sca/sca.html b/docs/nightly/_modules/CPAC/sca/sca.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/sca/utils.html b/docs/nightly/_modules/CPAC/sca/utils.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>

diff --git a/docs/nightly/_modules/CPAC/scrubbing/scrubbing.html b/docs/nightly/_modules/CPAC/scrubbing/scrubbing.html
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand centered" href="../../../index">
 
   <div class="sidebar-logo-container">
-    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.png" alt="Logo"/>
+    <img class="sidebar-logo" src="../../../_static/cpac_logo_vertical.svg" alt="Logo"/>
   </div>
 
   <span class="sidebar-brand-text">C-PAC 1.8.5.dev1 Beta documentation</span>