adding jupyter brain image

jupyter-brain/Dockerfile

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+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+FROM jupyter/scipy-notebook
+
+USER root
+
+# R pre-requisites
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    fonts-dejavu \
+    tzdata \
+    gfortran \
+    gcc \
+    libssl1.0.0 \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    zlib1g \
+    zlib1g-dev && apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+USER $NB_UID
+
+# R packages including IRKernel which gets installed globally.
+RUN conda config --system --append channels r && \
+    conda install --quiet --yes \
+    'rpy2' \
+    'r-base=3.4.3' \
+    'r-irkernel' \
+    'r-plyr' \
+    'r-devtools' \
+    'r-tidyverse' \
+    'r-shiny' \
+    'r-rmarkdown' \
+    'r-forecast' \
+    'r-rsqlite' \
+    'r-reshape2' \
+    'r-nycflights13' \
+    'r-caret' \
+    'r-rcurl' \
+    'r-crayon' \
+    'r-randomforest' \
+    'r-rmysql' \
+    'r-gplots' \
+    'r-gtools' \
+    'r-catools' \
+    && conda clean -tipsy && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+
+RUN echo "load.lib<-c('httr','jsonlite','dplyr','gplots','ggplot2','ggpubr','RColorBrewer','xml2','repr','VennDiagram'); install.lib<-load.lib[!load.lib %in% installed.packages()]; install.packages(install.lib,dependencies=TRUE, repos='http://cran.us.r-project.org', type='source')" | R --no-save
+RUN echo "source('https://www.bioconductor.org/biocLite.R'); load.s3<-c('maftools', 'phyloseq', 'DESeq2', 'dada2', 'vcfR'); install.s3<-load.s3[!load.s3 %in% installed.packages()]; for(s3 in install.s3) biocLite(s3);" | R --no-save
+
+USER root
+COPY resources/templates/ /opt/conda/lib/python3.6/site-packages/notebook/templates
+USER $NB_UID
+
+COPY resources/custom.js /home/$NB_USER/.jupyter/custom/
+COPY resources/jupyter_notebook_config.py /home/$NB_USER/.jupyter/tmp.py
+RUN cat /home/$NB_USER/.jupyter/tmp.py >> /home/$NB_USER/.jupyter/jupyter_notebook_config.py && rm /home/$NB_USER/.jupyter/tmp.py
+
+
+# this section is based off of: https://github.com/uc-cdis/bc-cwl/blob/master/brainCommonPipelineDocker4CWL/docker-freesurfer-master/Dockerfile
+USER root
+
+COPY license /usr/local/freesurfer/license.txt
+
+ENV FREESURFER_HOME /usr/local/freesurfer
+ENV FMRI_ANALYSIS_DIR /usr/local/freesurfer/fsfast
+ENV FSFAST_HOME /usr/local/freesurfer/fsfast
+ENV FUNCTIONALS_DIR /usr/local/freesurfer/sessions
+ENV LOCAL_DIR /usr/local/freesurfer/local
+ENV MINC_BIN_DIR /usr/local/freesurfer/mni/bin
+ENV MINC_LIB_DIR /usr/local/freesurfer/mni/lib
+ENV MNI_DATAPATH /usr/local/freesurfer/mni/data
+ENV MNI_DIR /usr/local/freesurfer/mni
+ENV MNI_PERL5LIB /usr/local/freesurfer/mni/share/perl5
+ENV PERL5LIB /usr/local/freesurfer/mni/share/perl5
+ENV SUBJECTS_DIR /usr/local/freesurfer/subjects
+ENV PATH $PATH:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+
+ADD extract_subfields.sh /mnt/
+ADD initialize_subDir.sh /mnt/
+ADD extract_subcortical.sh /mnt/
+ADD outlierDetection.sh /mnt/
+
+RUN apt-get update && apt-get install -y --no-install-recommends curl tar tcsh libglu1-mesa libgomp1 libjpeg62 libxext6 libxtst6  libxt6 libxt-dev libxmu6 \
+  && curl ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar xvz -C /usr/local \
+  && apt-get install -y --no-install-recommends jq bc libsys-hostname-long-perl && ldconfig && mkdir -p /N/u /N/home /N/dc2 /N/soft \
+  && curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bLinux.tar.gz" -o "/usr/local/freesurfer/runtime2012b.tar.gz" \
+  && tar xf /usr/local/freesurfer/runtime2012b.tar.gz -C /usr/local/freesurfer/ \
+  && /bin/rm /usr/local/freesurfer/runtime2012b.tar.gz \
+  && apt-get remove -y curl \
+  && rm -rf /var/lib/apt/lists/*
+
+
+USER $NB_UID

jupyter-brain/README.md

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+# TL;DR
+
+Jupyter notebook with freesurfer installed.
+
+## Notes
+
+Freesurfer is big (11 Gig), so this docker image is big, so the `quay` build fails,
+so we for now just build locally, tag, and push to quay.io/cdis/jupyterbrain

jupyter-brain/build.sh

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+docker build -t brainlife/freesurfer . && \
+    docker tag brainlife/freesurfer brainlife/freesurfer:6.0.0 && \
+    docker push brainlife/freesurfer

jupyter-brain/docker_command_backup.txt

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+docker run -it --rm -v /Users/xingyankuang/Downloads/docker-freesurfer-master:/input brainlife/freesurfer mri_convert input/sub-01_T1w.nii.gz input/test.mgz
+docker run -it --rm -v /Users/xingyankuang/Downloads/subjectDir:/usr/local/freesurfer/subjects brainlife/freesurfer recon-all -s subj10159 -hippocampal-subfields-T1

jupyter-brain/extract_subcortical.sh

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+#!/bin/bash
+cd $1
+outputF=$3
+subList=$2
+#bash
+echo "SubjID,LLatVent,RLatVent,Lthal,Rthal,Lcaud,Rcaud,Lput,Rput,Lpal,Rpal,Lhippo,Rhippo,Lamyg,Ramyg,Laccumb,Raccumb,ICV" > $outputF
+for sub_id in $(cat $subList); do
+#for sub_id in `ls -d subj*`; do 
+printf "%s,"  "${sub_id}" >> $outputF
+for x in Left-Lateral-Ventricle Right-Lateral-Ventricle Left-Thalamus-Proper Right-Thalamus-Proper Left-Caudate Right-Caudate Left-Putamen Right-Putamen Left-Pallidum Right-Pallidum Left-Hippocampus Right-Hippocampus Left-Amygdala Right-Amygdala Left-Accumbens-area Right-Accumbens-area; do
+printf "%g," `grep  ${x} ${sub_id}/stats/aseg.stats | awk '{print $4}'` >> $outputF
+done
+printf "%g" `cat ${sub_id}/stats/aseg.stats | grep IntraCranialVol | awk -F, '{print $4}'` >> $outputF
+echo "" >> $outputF
+done
+

jupyter-brain/extract_subfields.sh

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+#!/bin/bash
+cd $1
+outputF=$3
+subList=$2
+echo 'SubjID,L_Hippocampal_tail,L_subiculum,L_CA1,L_hippocampal-fissure,L_presubiculum,L_parasubiculum,L_molecular_layer_HP,L_GC-ML-DG,L_CA3,L_CA4,L_fimbria,L_HATA,L_Whole_hippocampus,R_Hippocampal_tail,R_subiculum,R_CA1,R_hippocampal-fissure,R_presubiculum,R_parasubiculum,R_molecular_layer_HP,R_GC-ML-DG,R_CA3,R_CA4,R_fimbria,R_HATA,R_Whole_hippocampus,Lhippo,Rhippo,eTIV,Brain,TotalGM' > $outputF
+
+#for subj_id in $(ls -d 00*); do # approach A: create the list here, e. g. for rootname 'WG_' in this example
+for subj_id in $(cat $subList); do # approach B: use an explicit list
+printf "%s,"  "${subj_id}" >> $outputF
+
+
+
+for x in Hippocampal_tail subiculum CA1 hippocampal-fissure presubiculum parasubiculum molecular_layer_HP GC-ML-DG CA3 CA4 fimbria HATA Whole_hippocampus; do
+printf "%g," `grep -w ${x} ${subj_id}/mri/lh.hippoSfVolumes-T1.v10.txt | awk '{print $2}'` >> $outputF
+done
+
+for x in Hippocampal_tail subiculum CA1 hippocampal-fissure presubiculum parasubiculum molecular_layer_HP GC-ML-DG CA3 CA4 fimbria HATA Whole_hippocampus; do
+printf "%g," `grep -w ${x} ${subj_id}/mri/rh.hippoSfVolumes-T1.v10.txt | awk '{print $2}'` >> $outputF
+done
+
+
+for x in Left-Hippocampus Right-Hippocampus; do
+printf "%g," `grep  ${x} ${subj_id}/stats/aseg.stats | awk '{print $4}'` >> $outputF
+done
+
+printf "%g," `cat ${subj_id}/stats/aseg.stats | grep IntraCranialVol | awk -F, '{print $4}'` >> $outputF
+printf "%g," `cat ${subj_id}/stats/aseg.stats | grep 'Brain Segmentation Volume,' | awk -F, '{print $4}'` >> $outputF
+printf "%g" `cat ${subj_id}/stats/aseg.stats | grep  'Total gray matter volume' | awk -F, '{print $4}'` >> $outputF
+
+echo "" >> $outputF
+
+done
+#/bin/bash extract_subfields.sh subjectDir_test  list_subjects.txt hippo_subfield_volume

jupyter-brain/initialize_subDir.sh

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+#!/bin/bash
+dir_name=$1
+
+cp -r /usr/local/freesurfer/subjects/fsaverage  $dir_name

jupyter-brain/license

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+[email protected] 29511 *CPmh9xvKQKHE FSg0ijTusqaQc

jupyter-brain/outlierDetection.sh

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+#!/bin/bash
+summary_state=$1
+extracted_volumes=$2
+out=$3
+echo "Region,MNminus1.5IQI,MNplus1.5IQI" > IQI_range.csv
+#sed '1d' $summary_state | grep -v "Assym" | grep -v "Avg_"  | awk ' { print $1","$4-2.698*$5","$4+2.698*$5 } ' >> IQI_range.csv
+sed '1d' $summary_state | grep -v "Assym" | grep -v "Avg_"  | awk ' { print $1","$4-2.3*$5","$4+2.3*$5 } ' >> IQI_range.csv
+N_regions=`cat $extracted_volumes | head -n 1 | awk -F "," ' { print NF } '`
+
+echo ' ' > $out
+for (( c=2; c<=$N_regions; c++))
+do roi=`cat $extracted_volumes | head -n 1 | awk -F "," ' { print $'$c' } '`
+IQI_low=`cat IQI_range.csv | grep $roi | awk -F "," ' { print $2 }'`
+IQI_high=`cat IQI_range.csv | grep $roi | awk -F "," ' { print $3 }'`
+IQI_low_int=`printf "%10.0f\n" $IQI_low`
+IQI_high_int=`printf "%10.0f\n" $IQI_high`
+echo "Looking for subjects with "$roi" volumes outside of "$IQI_low":"$IQI_high >> $out
+cnt=1
+for textline in `sed '1d' $extracted_volumes | awk -F "," ' { print $'$c' } '`
+do cnt=`echo $cnt+1 | bc `
+textline_int=`printf "%10.0f\n" $textline`
+if [ $textline_int -gt $IQI_high_int ];
+then sid=`cat $extracted_volumes | head -n $cnt | tail -n 1 | awk -F "," ' { print $1 } '`
+echo $sid" has a "$roi" of "$textline", this volume is high" >> $out
+fi
+if [ $textline_int -lt $IQI_low_int ];
+then sid=`cat $extracted_volumes | head -n $cnt | tail -n 1 | awk -F "," ' { print $1 } '`
+echo $sid" has a "$roi" of "$textline", this volume is low" >> $out
+fi
+done
+done
+#cat $out | grep "has" |  awk -F/ ' { print $NF } ' | awk ' { print $1 } '| sort | uniq
+

jupyter-brain/resources/custom.js

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+define(['base/js/namespace'], function(Jupyter){
+    Jupyter._target = '_self';
+})

jupyter-brain/resources/jupyter_notebook_config.py

@@ -0,0 +1,6 @@
+c.NotebookApp.tornado_settings = {
+    'headers': {
+        'Content-Security-Policy':
+        "frame-ancestors 'self'"
+    }
+}

jupyter-brain/resources/templates/page.html

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+<!DOCTYPE HTML>
+<html>
+
+<head>
+    <meta charset="utf-8">
+
+    <title>{% block title %}Jupyter Notebook{% endblock %}</title>
+    {% block favicon %}<link id="favicon" rel="shortcut icon" type="image/x-icon" href="{{static_url("base/images/favicon.ico") }}">{% endblock %}
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <link rel="stylesheet" href="{{static_url("components/jquery-ui/themes/smoothness/jquery-ui.min.css") }}" type="text/css" />
+    <link rel="stylesheet" href="{{static_url("components/jquery-typeahead/dist/jquery.typeahead.min.css") }}" type="text/css" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+    {% block stylesheet %}
+    <link rel="stylesheet" href="{{ static_url("style/style.min.css") }}" type="text/css"/>
+    {% endblock %}
+    <link rel="stylesheet" href="{{ base_url }}custom/custom.css" type="text/css" />
+    <script src="{{static_url("components/es6-promise/promise.min.js")}}" type="text/javascript" charset="utf-8"></script>
+    <script src="{{static_url('components/preact/index.js')}}" type="text/javascript"></script>
+    <script src="{{static_url('components/proptypes/index.js')}}" type="text/javascript"></script>
+    <script src="{{static_url('components/preact-compat/index.js')}}" type="text/javascript"></script>
+    <script src="{{static_url('components/requirejs/require.js') }}" type="text/javascript" charset="utf-8"></script>
+    <script>
+      require.config({
+          {% if version_hash %}
+          urlArgs: "v={{version_hash}}",
+          {% endif %}
+          baseUrl: '{{static_url("", include_version=False)}}',
+          paths: {
+            'auth/js/main': 'auth/js/main.min',
+            custom : '{{ base_url }}custom',
+            nbextensions : '{{ base_url }}nbextensions',
+            kernelspecs : '{{ base_url }}kernelspecs',
+            underscore : 'components/underscore/underscore-min',
+            backbone : 'components/backbone/backbone-min',
+            jed: 'components/jed/jed',
+            jquery: 'components/jquery/jquery.min',
+            json: 'components/requirejs-plugins/src/json',
+            text: 'components/requirejs-text/text',
+            bootstrap: 'components/bootstrap/js/bootstrap.min',
+            bootstraptour: 'components/bootstrap-tour/build/js/bootstrap-tour.min',
+            'jquery-ui': 'components/jquery-ui/jquery-ui.min',
+            moment: 'components/moment/min/moment-with-locales',
+            codemirror: 'components/codemirror',
+            termjs: 'components/xterm.js/xterm',
+            typeahead: 'components/jquery-typeahead/dist/jquery.typeahead.min',
+          },
+          map: { // for backward compatibility
+              "*": {
+                  "jqueryui": "jquery-ui",
+              }
+          },
+          shim: {
+            typeahead: {
+              deps: ["jquery"],
+              exports: "typeahead"
+            },
+            underscore: {
+              exports: '_'
+            },
+            backbone: {
+              deps: ["underscore", "jquery"],
+              exports: "Backbone"
+            },
+            bootstrap: {
+              deps: ["jquery"],
+              exports: "bootstrap"
+            },
+            bootstraptour: {
+              deps: ["bootstrap"],
+              exports: "Tour"
+            },
+            "jquery-ui": {
+              deps: ["jquery"],
+              exports: "$"
+            }
+          },
+          waitSeconds: 30,
+      });
+
+      require.config({
+          map: {
+              '*':{
+                'contents': '{{ contents_js_source }}',
+              }
+          }
+      });
+
+      // error-catching custom.js shim.
+      define("custom", function (require, exports, module) {
+          try {
+              var custom = require('custom/custom');
+              console.debug('loaded custom.js');
+              return custom;
+          } catch (e) {
+              console.error("error loading custom.js", e);
+              return {};
+          }
+      })
+
+    document.nbjs_translations = {{ nbjs_translations|safe }};
+    document.documentElement.lang = navigator.language.toLowerCase();
+    </script>
+
+    {% block meta %}
+    {% endblock %}
+
+</head>
+
+<body class="{% block bodyclasses %}{% endblock %}"
+ {% block params %}
+  {% if logged_in and token %}
+    data-jupyter-api-token="{{token | urlencode}}"
+  {% endif %}
+ {% endblock params %}
+dir="ltr">
+
+<noscript>
+    <div id='noscript'>
+      {% trans %}Jupyter Notebook requires JavaScript.{% endtrans %}<br>
+      {% trans %}Please enable it to proceed. {% endtrans %}
+  </div>
+</noscript>
+
+<div id="header">
+  <div id="header-container" class="container">
+  <div id="ipython_notebook" class="nav navbar-brand"><a href="{{default_url}}
+    {%- if logged_in and token -%}?token={{token}}{%- endif -%}" title='{% trans %}dashboard{% endtrans %}'>
+      {% block logo %}<img src='{{static_url("base/images/logo.png") }}' alt='Jupyter Notebook'/>{% endblock %}
+  </a></div>
+
+  {% block headercontainer %}
+  {% endblock %}
+
+  </div>
+  <div class="header-bar"></div>
+
+  {% block header %}
+  {% endblock %}
+</div>
+
+<div id="site">
+{% block site %}
+{% endblock %}
+</div>
+
+{% block after_site %}
+{% endblock %}
+
+{% block script %}
+{% endblock %}
+
+<script type='text/javascript'>
+  function _remove_token_from_url() {
+    if (window.location.search.length <= 1) {
+      return;
+    }
+    var search_parameters = window.location.search.slice(1).split('&');
+    for (var i = 0; i < search_parameters.length; i++) {
+      if (search_parameters[i].split('=')[0] === 'token') {
+        // remote token from search parameters
+        search_parameters.splice(i, 1);
+        var new_search = '';
+        if (search_parameters.length) {
+          new_search = '?' + search_parameters.join('&');
+        }
+        var new_url = window.location.origin + 
+                      window.location.pathname + 
+                      new_search + 
+                      window.location.hash;
+        window.history.replaceState({}, "", new_url);
+        return;
+      }
+    }
+  }
+  _remove_token_from_url();
+</script>
+</body>
+
+</html>