MIAL Super-Resolution Toolkit v2.0

.dockerignore

@@ -0,0 +1,33 @@
+*.pklz
+*.pyc
+*.npz
+*.xdebug_tkmedit
+*.mp4
+atom-config.txt
+
+.DS_Store?
+.DS_Store
+ehthumbs.db
+Icon?
+Thumbs.db
+
+docs
+docs/*
+
+docker
+docker/*
+
+debian
+debian/*
+
+dist
+dist/*
+
+build
+build/*
+
+_build
+_static
+_templates
+
+*.ipynb_checkpoints

.gitignore

@@ -9,6 +9,11 @@
 *.*~
 *.save
 
+# python #
+#################################
+*.ipynb_checkpoints
+*__pycache__
+
 # Generated testing images #
 ############################
 superresolution.nii.gz
@@ -71,3 +76,7 @@ bin
 bin-dbg
 Bin
 RECON
+
+# Data derivatives  #
+#####################
+data/derivatives/mialsrtk*

.zenodo.json

@@ -3,13 +3,11 @@
     "keywords": [
       "fetal",
       "neuroimaging",
-      "workflow",
       "pipeline",
       "super-resolution",
       "registration",
       "MRI",
-      "BIDS",
-      "BIDS-App"
+      "BIDS"
     ],
     "publication_date": "2019-03-19",
     "creators": [
@@ -18,6 +16,10 @@
         "affiliation": "Department of Radiology, Lausanne University Hospital (CHUV), Switzerland",
         "orcid": "0000-0002-4441-899X"
       },
+      {
+        "name": "Bresson, Xavier",
+        "affiliation": "Data Science and AI Center (DSAIR), Nanyang Technological University (NTU), Singapore"
+      },
       {
         "name": "Bach Cuadra, Meritxell",
         "affiliation": "Department of Radiology, Lausanne University Hospital (CHUV), Switzerland",

Dockerfile

@@ -0,0 +1,86 @@
+FROM ubuntu:14.04
+
+RUN apt-get update && \
+    apt-get install software-properties-common -y && \
+    apt-add-repository ppa:saiarcot895/myppa -y && \
+    apt-get update && \
+    apt-get -y install apt-fast \
+    && apt-fast install -y \
+    build-essential \
+    exfat-fuse \
+    exfat-utils \
+    npm \
+    curl \
+    bzip2 \
+    xvfb \
+    x11-apps \
+    git \
+    gcc-4.8 \
+        g++-4.8 \
+        cmake \
+        libtclap-dev \
+        libinsighttoolkit4.5 \
+        libinsighttoolkit4-dev \
+        libvtk5-dev \
+        libvtk5-qt4-dev \
+        libvtk5.8 \
+        libvtk5.8-qt4 \
+        tcl-vtk \
+        libvtk-java \
+        python-vtk \
+        python-vtkgdcm \
+        libncurses5  \
+        libncurses5-dev \
+    libann-dev \
+    python-qt4 \
+    python-nibabel \
+    python-numpy \
+    python-scipy \
+    python-matplotlib && \
+    curl -sSL https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -o /tmp/miniconda.sh && \
+    bash /tmp/miniconda.sh -bfp /opt/conda && \
+    rm -rf /tmp/miniconda.sh && \
+    apt-get clean
+
+
+ENV PATH /opt/conda/bin:$PATH
+
+RUN conda update conda && \
+    conda clean --all --yes
+
+RUN groupadd -r -g 1000 mialsrtk && \
+    useradd -r -M -u 1000 -g mialsrtk mialsrtk
+
+WORKDIR /opt/mialsuperresolutiontoolkit
+ADD . /opt/mialsuperresolutiontoolkit
+RUN mkdir build
+WORKDIR /opt/mialsuperresolutiontoolkit/build
+
+RUN cd /opt/mialsuperresolutiontoolkit/build \
+    && cmake -D CMAKE_BUILD_TYPE=Release -D CMAKE_INSTALL_PREFIX=/usr/local -D USE_OMP:BOOL=ON ../src \ 
+    && make -j2 && sudo make install && cd .. 
+
+# Make MIALSRTK happy
+ENV BIN_DIR "/usr/local/bin" 
+ENV PATH ${BIN_DIR}:$PATH
+
+ENV BIN_DIR "/usr/local/bin" 
+ENV DISPLAY :0
+
+ARG BUILD_DATE
+ARG VCS_REF
+ARG VERSION
+
+#Metadata
+LABEL org.label-schema.build-date=$BUILD_DATE
+LABEL org.label-schema.name="MIAL Super-Resolution ToolKit Ubuntu 14.04"
+LABEL org.label-schema.description="Computing environment of the MIAL Super-Resolution BIDS App based on Ubuntu 14.04."
+LABEL org.label-schema.url="https://mialsuperresolutiontoolkit.readthedocs.io"
+LABEL org.label-schema.vcs-ref=$VCS_REF
+LABEL org.label-schema.vcs-url="https://github.com/sebastientourbier/mialsuperresolutiontoolkit"
+LABEL org.label-schema.version=$VERSION
+LABEL org.label-schema.maintainer="Sebastien Tourbier <sebastien.tourbier@alumni.epfl.ch>"
+LABEL org.label-schema.vendor="Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland"
+LABEL org.label-schema.schema-version="1.0"
+LABEL org.label-schema.docker.cmd="docker run --rm -v ~/data/bids_dataset:/tmp -t sebastientourbier/mialsuperresolutiontoolkit-ubuntu16.04:${VERSION}"
+

build_bidsapp.sh

@@ -0,0 +1,24 @@
+#! /bin/sh
+CMP_BUILD_DATE=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
+echo $CMP_BUILD_DATE
+
+VERSION=v$(python get_version.py)
+echo $VERSION
+
+VCS_REF=$(git rev-parse --verify HEAD)
+echo $VCS_REF
+
+MAIN_DOCKER="sebastientourbier/mialsuperresolutiontoolkit-ubuntu14.04:${VERSION}"
+echo $MAIN_DOCKER
+
+docker build --rm --build-arg BUILD_DATE=$CMP_BUILD_DATE \
+				  --build-arg VCS_REF=$VCS_REF \
+				  --build-arg VERSION=$VERSION \
+				  -t "${MAIN_DOCKER}" . \
+
+
+docker build --no-cache --rm --build-arg BUILD_DATE=$CMP_BUILD_DATE \
+                             --build-arg VERSION=$VERSION \
+                             --build-arg VCS_REF=$VCS_REF \
+                             --build-arg MAIN_DOCKER=$MAIN_DOCKER \
+                             -t sebastientourbier/mialsuperresolutiontoolkit-bidsapp:${VERSION} ./docker/bidsapp

build_jupyter.sh

@@ -0,0 +1,25 @@
+#! /bin/sh
+CMP_BUILD_DATE=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
+echo $CMP_BUILD_DATE
+
+VERSION=v$(python get_version.py)
+echo $VERSION
+
+VCS_REF=$(git rev-parse --verify HEAD)
+echo $VCS_REF
+
+MAIN_DOCKER="sebastientourbier/mialsuperresolutiontoolkit-ubuntu14.04:${VERSION}"
+echo $MAIN_DOCKER
+
+docker build --rm --build-arg BUILD_DATE=$CMP_BUILD_DATE \
+				  --build-arg VCS_REF=$VCS_REF \
+				  --build-arg VERSION=$VERSION \
+				  -t "${MAIN_DOCKER}" . \
+
+JUPYTER_DOCKER="sebastientourbier/mialsuperresolutiontoolkit-jupyter:${VERSION}"
+
+docker build --rm --build-arg BUILD_DATE=$CMP_BUILD_DATE \
+                             --build-arg VERSION=$VERSION \
+                             --build-arg VCS_REF=$VCS_REF \
+                             --build-arg MAIN_DOCKER=$MAIN_DOCKER \
+                             -t "${JUPYTER_DOCKER}" ./docker/jupyter

data/.bidsignore

@@ -0,0 +1,3 @@
+{
+	"ignoredFiles": ["*/tmp/**"]
+}

data/CHANGES

@@ -0,0 +1,3 @@
+1.0.0 2019-05-10
+
+- initial release

data/README

@@ -0,0 +1,10 @@
+This sample BIDS dataset contains a set of three orthogonal MRI 
+with anisotropic resolution (1x1x2mm^3) of the fetal brain of subject "sub-01"
+acquired with a fast multi-slice sequence.
+
+Manually drawn brain masks can be found in derivatives/manual_masks/sub-01/anat folder
+
+The text file listing the scans used by the supperresolution_pipeline.sh script 
+can be found in code/ as sub-01_ses-01_scans.txt
+
+- Sebastien Tourbier (May 10, 2019)

data/code/batch_list.txt

@@ -0,0 +1 @@
+sub-01 ses-01 0.75 0.01 

data/code/create_dataset_description_json.sh

@@ -0,0 +1,23 @@
+#!/bin/sh
+# 
+# Usage:
+# 		sh create_dataset_description_json output.json v1.1.0
+# 
+# Author: Sebastien Tourbier
+# 
+###################################################################
+
+OUTPUT_JSON=$1
+
+(
+cat <<EOF
+{
+    "PipelineDescription": {
+		"Name": "MIAL Super-Resolution ToolKit",
+		"Version":   "$2",
+		"CodeURL":   "https://github.com/sebastientourbier/mialsuperresolutiontoolkit"
+	}
+}
+
+EOF
+) > $OUTPUT_JSON

data/code/create_scan_preproc_json.sh

@@ -0,0 +1,25 @@
+#!/bin/sh
+# 
+# Usage:
+# 		sh create_scan_preproc_json output.json source.nii.gz
+# 
+# Author: Sebastien Tourbier
+# 
+###################################################################
+
+OUTPUT_JSON=$1
+
+(
+cat <<EOF
+{
+	"Description": "Preprocessed image used as input to the Super-Resolution algorithm",
+    "Sources": "$2",
+    "CustomMetaData": {
+		"Reorient": true,
+		"Intensity standardization":   true,
+		"Bias Field Correction": true
+	}
+}
+
+EOF
+) > $OUTPUT_JSON

data/code/participants_params.json

@@ -0,0 +1,9 @@
+{
+  "01": [
+    { "srID":1,
+      "stacksOrder": [1, 3, 5, 5, 4, 6],
+      "paramTV": { 
+        "lambdaTV": 0.75, 
+        "deltatTV": 0.01 }
+    }]
+}

data/code/sub-01_ses-01_scans.txt

@@ -0,0 +1,6 @@
+run-1 axial
+run-3 coronal
+run-5 sagittal
+run-2 axial
+run-4 coronal
+run-6 sagittal

data/code/sub-01_ses-02_scans.txt

@@ -0,0 +1,6 @@
+run-1 axial
+run-2 coronal
+run-3 sagittal
+run-4 coronal
+run-5 sagittal
+run-6 sagittal