deploy: bd65b36

dev/index.html

@@ -418,7 +418,7 @@ <h3>Segmentation Modules<a class="headerlink" href="#segmentation-modules" title
 <li><p>calculates volume statistics corrected for partial volume effects (skipped if <code class="docutils literal notranslate"><span class="pre">--no_biasfield</span></code> is passed).</p></li>
 </ul>
 </li>
-<li><p><code class="docutils literal notranslate"><span class="pre">hypothal</span></code>: <a class="reference internal" href="scripts/hypvinn.html"><span class="doc std std-ref">HypVINN</span></a> for hypothalamus subsegmentation (deactivate with <code class="docutils literal notranslate"><span class="pre">no_hypothal</span></code>)</p>
+<li><p><code class="docutils literal notranslate"><span class="pre">hypothal</span></code>: <a class="reference internal" href="scripts/hypvinn.html"><span class="doc std std-ref">HypVINN</span></a> for hypothalamus subsegmentation (deactivate with <code class="docutils literal notranslate"><span class="pre">--no_hypothal</span></code>)</p>
 <ul class="simple">
 <li><p>outputs a hypothalamic subsegmentation including 3rd ventricle, c. mammilare, fornix and optic tracts.</p></li>
 <li><p>a T1w image is highly recommended (<a class="reference internal" href="#"><span class="doc std std-ref">notes on input images</span></a>), supports high-res (up to 0.7mm, but experimental beyond that).</p></li>

dev/overview/intro.html

@@ -396,7 +396,7 @@ <h3>Installation<a class="headerlink" href="#installation" title="Link to this h
 <li><p>In a container (<a class="reference internal" href="INSTALL.html#singularity"><span class="std std-ref">Singularity</span></a> or <a class="reference internal" href="INSTALL.html#docker"><span class="std std-ref">Docker</span></a>) (OS: <a class="reference internal" href="INSTALL.html#linux"><span class="std std-ref">Linux</span></a>, <a class="reference internal" href="INSTALL.html#windows"><span class="std std-ref">Windows</span></a>, <a class="reference internal" href="INSTALL.html#docker-currently-only-supported-for-intel-cpus"><span class="std std-ref">MacOS on Intel</span></a>),</p></li>
 <li><p>As a <a class="reference internal" href="INSTALL.html#native-ubuntu-20-04-or-ubuntu-22-04"><span class="std std-ref">native install</span></a> (all OS for segmentation part).</p></li>
 </ol>
-<p>We recommended you use Singularity or Docker on a Linux host system with a GPU. The images we provide on <a class="reference external" href="https://hub.docker.com/r/deepmi/fastsurfer">DockerHub</a> conveniently include everything needed for FastSurfer. You will also need a <a class="reference external" href="https://surfer.nmr.mgh.harvard.edu/fswiki/License">FreeSurfer license file</a> for the <a class="reference internal" href="../index.html"><span class="doc std std-ref">Surface pipeline</span></a>. We have detailed per-OS Installation instructions in the <a class="reference internal" href="INSTALL.html"><span class="std std-doc">INSTALL.md file</span></a>.</p>
+<p>We recommended you use Singularity or Docker on a Linux host system with a GPU. The images we provide on <a class="reference external" href="https://hub.docker.com/r/deepmi/fastsurfer">DockerHub</a> conveniently include everything needed for FastSurfer. You will also need a <a class="reference external" href="https://surfer.nmr.mgh.harvard.edu/fswiki/License">FreeSurfer license</a> file for the <a class="reference internal" href="../index.html"><span class="doc std std-ref">Surface pipeline</span></a>. We have detailed per-OS Installation instructions in the <a class="reference internal" href="INSTALL.html"><span class="std std-doc">INSTALL.md</span></a> file.</p>
 </section>
 <section id="usage">
 <h3>Usage<a class="headerlink" href="#usage" title="Link to this heading">¶</a></h3>

dev/scripts/SLURM.html

@@ -426,7 +426,7 @@ <h2>Usage<a class="headerlink" href="#usage" title="Link to this heading">¶</a>
   Note: files will be copied here only after all jobs have finished, so most IO happens on
   a work directory, which can use IO-optimized cluster storage (see --work).
 --work: directory with fast filesystem on cluster
-  (default: $HPCWORK/fastsurfer-processing/20241029-154855)
+  (default: $HPCWORK/fastsurfer-processing/20241102-101634)
   NOTE: THIS SCRIPT considers this directory to be owned by this script and job!
   No modifications should be made to the directory after the job is started until it is
   finished (if the job fails, cleanup of this directory may be necessary) and it should be

stable/scripts/SLURM.html

@@ -426,7 +426,7 @@ <h2>Usage<a class="headerlink" href="#usage" title="Link to this heading">¶</a>
   Note: files will be copied here only after all jobs have finished, so most IO happens on
   a work directory, which can use IO-optimized cluster storage (see --work).
 --work: directory with fast filesystem on cluster
-  (default: $HPCWORK/fastsurfer-processing/20241029-130320)
+  (default: $HPCWORK/fastsurfer-processing/20241108-095037)
   NOTE: THIS SCRIPT considers this directory to be owned by this script and job!
   No modifications should be made to the directory after the job is started until it is
   finished (if the job fails, cleanup of this directory may be necessary) and it should be
@@ -490,7 +490,7 @@ <h2>Usage<a class="headerlink" href="#usage" title="Link to this heading">¶</a>
      (one of the above).
   default: slurm default partition
 --time: a per-subject time limit for individual steps, must be number in minutes:
-   --time seg=&lt;timelimit&gt;: time limit for the segmentation pipeline (per subject), default: seg=5 (5min).
+   --time seg=&lt;timelimit&gt;: time limit for the segmentation pipeline (per subject), default: seg=10 (10min).
    --time surf=&lt;timelimit&gt;: time limit for the surface reconstruction (per subject), default: surf=180 (180min)
 --email: email address to send slurm status updates.