add a Dockerfile

Dockerfile

@@ -0,0 +1,49 @@
+## Build Docker image for execution of dhcp pipelines within a Docker
+## container with all modules and applications available in the image
+##
+## How to build the image:
+## - Change to top-level directory of structural-pipeline source tree
+## - Run "docker build --build-arg VCS_REF=`git rev-parse --short HEAD` -t <user>/structural-pipeline:latest ."
+##
+## Upload image to Docker Hub:
+## - Log in with "docker login" if necessary
+## - Push image using "docker push <user>/structural-pipeline:latest"
+##
+
+FROM ubuntu:xenial
+MAINTAINER John Cupitt <[email protected]>
+LABEL Description="dHCP structural-pipeline" Vendor="BioMedIA"
+
+# Git repository and commit SHA from which this Docker image was built
+# (see https://microbadger.com/#/labels)
+ARG VCS_REF
+LABEL org.label-schema.vcs-ref=$VCS_REF \
+      org.label-schema.vcs-url="https://github.com/DevelopingHCP/structural-pipeline"
+
+# No. of threads to use for build (--build-arg THREADS=8)
+# By default, all available CPUs are used. When a Docker Machine is used,
+# set the number of CPUs in the VirtualBox VM Settings.
+ARG THREADS
+
+# install prerequsites
+# - FSL
+# - build tools
+
+RUN apt-get update 
+RUN apt-get install -y apt-utils wget 
+RUN wget -O- http://neuro.debian.net/lists/artful.de-m.full | tee /etc/apt/sources.list.d/neurodebian.sources.list 
+RUN apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 
+RUN apt-get update 
+RUN apt-get install -y \
+	fsl-complete \
+	g++-5 git cmake unzip bc python python-contextlib2 \
+	libtbb-dev libboost-dev zlib1g-dev libxt-dev libexpat1-dev \
+	libgstreamer1.0-dev libqt4-dev
+
+COPY . /usr/src/structural-pipeline
+RUN ls /usr/src/structural-pipeline \
+    && NUM_CPUS=${THREADS:-`cat /proc/cpuinfo | grep processor | wc -l`} \
+    && echo "Maximum number of build threads = $NUM_CPUS" \
+    && cd /usr/src/structural-pipeline \
+    && ./setup.sh -j $NUM_CPUS
+

README.md

@@ -23,6 +23,56 @@ A. Makropoulos and E. C. Robinson et al. "The Developing Human Connectome Projec
 ## License
 The dHCP structural pipeline is distributed under the terms outlined in LICENSE.txt
 
+## Install and run with docker
+You can build the pipeline in a docker container. This will work on any
+version of any platform, is automated, and fairly simple. First, install
+docker:
+
+https://docs.docker.com/engine/installation/
+
+Then in the top directory of `structural-pipeline`, use git to switch to the
+branch you want to build, and enter:
+
+```
+# docker build -t <user>/structural-pipeline:latest .
+```
+
+Substituting `<user>` for your username. This command must be run as root. 
+
+This will create a single docker image called
+`<user>/structural-pipeline:latest` containing all the required files 
+and all required dependencies. 
+
+You can then execute the pipeline like this (for example):
+
+```
+# docker run --rm -t -v $PWD/data:/data \
+    -u $(id -u <user>):$(id -g <user>) \
+    <user>/structural-pipeline:latest \
+    bash -c ". /etc/fsl/fsl.sh; \
+        cd /usr/src/structural-pipeline; \
+        ./dhcp-pipeline.sh subject1 session1 44 \
+            -d /data -T2 /data/sub-CC00183XX11_ses-60300_T2w.nii.gz -t 8"
+```
+
+Again, this must be run as root. This will mount the subdirectory `data` of
+your current directory as `/data` in the container, then execute the pipeline
+on the file `sub-CC00183XX11_ses-60300_T2w.nii.gz`. The output files will be
+written to the `data` subdirectory. 
+
+## Run interactively
+Handy for debugging:
+
+```
+# sudo docker run \
+    -v /home/john/pics/dhcp/data:/data \
+    -it john/structural-pipeline:latest /bin/bash
+```
+
+## Install locally
+If you want to work on the code of the pipeline, it can be more convenient to
+install locally to your machine. Only read on if you need to do a local
+install. 
 
 ## Dependencies
 #### 1. FSL

dhcp-pipeline.sh

@@ -1,5 +1,9 @@
 #!/bin/bash
 
+# fsl prefix ... this was blank for fsl4, but fsl5+ have a versioned command
+# prefix
+fslprefix=fsl5.0-
+
 usage()
 {
   base=$(basename "$0")
@@ -130,7 +134,7 @@ for modality in T1 T2;do
   if [ $noreorient -eq 1 ];then
     cp $mf $newf
   else
-    fslreorient2std $mf $newf
+    ${fslprefix}fslreorient2std $mf $newf
   fi
   eval "$modality=$newf"
 done