bids-apps · treanus · Sep 8, 2021 · Sep 8, 2021 · Sep 8, 2021 · Sep 8, 2021
diff --git a/Dockerfile b/Dockerfile
@@ -1,5 +1,8 @@
+# THIS DOCKERFILE IS BROKEN
+# it is being developed to incorporate synb0 and dev branch of MRtrix3
+
 FROM ubuntu:18.04
-MAINTAINER Robert E. Smith <robert.smith@florey.edu.au>
+LABEL org.opencontainers.image.authors="Robert E. Smith <robert.smith@florey.edu.au>"
 
 # Core system capabilities required
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
@@ -18,7 +21,8 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
     tcsh \
     tzdata \
     unzip \
-    wget
+    wget \
+    npm
 
 # PPA for newer version of nodejs, which is required for bids-validator
 RUN curl -sL https://deb.nodesource.com/setup_12.x -o nodesource_setup.sh && \
@@ -58,20 +62,31 @@ RUN wget -qO- https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/frees
     --exclude='freesurfer/lib/qt'
 RUN echo "cHJpbnRmICJyb2JlcnQuc21pdGhAZmxvcmV5LmVkdS5hdVxuMjg1NjdcbiAqQ3FLLjFwTXY4ZE5rXG4gRlNvbGRZRXRDUFZqNlxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
 RUN apt-get install -y ants=2.2.0-1ubuntu1
+
+
 # FSL installer appears to now be ready for use with version 6
 # eddy is also now included in FSL6
-RUN wget -q http://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py && \
-    chmod 775 fslinstaller.py && \
-    python2 /fslinstaller.py -d /opt/fsl -V 6.0.4 -q && \
-    rm -f /fslinstaller.py
-RUN which immv || ( echo "FSLPython not properly configured; re-running" && rm -rf /opt/fsl/fslpython && /opt/fsl/etc/fslconf/fslpython_install.sh -f /opt/fsl || ( cat /tmp/fslpython*/fslpython_miniconda_installer.log && exit 1 ) )
+#RUN wget -q http://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py && \
+#    chmod 775 fslinstaller.py && \
+#    python2 /fslinstaller.py -d /opt/fsl -V 6.0.4 -q && \
+#    rm -f /fslinstaller.py
+#RUN which immv || ( echo "FSLPython not properly configured; re-running" && rm -rf /opt/fsl/fslpython && /opt/fsl/etc/fslconf/fslpython_install.sh -f /opt/fsl || ( cat /tmp/fslpython*/fslpython_miniconda_installer.log && exit 1 ) )
+FROM buildpack-deps:buster AS base-builder
+FROM base-builder as fsl-installer
+WORKDIR /opt/fsl
+RUN curl -fsSL https://osf.io/dv258/download \
+    | tar xz --strip-components 1
+
+# ROBEX
 RUN wget -qO- "https://www.nitrc.org/frs/download.php/5994/ROBEXv12.linux64.tar.gz//?i_agree=1&download_now=1" | \
     tar zx -C /opt
-RUN npm install -gq bids-validator@1.5.3
+
+# BIDS validator
+#RUN npm install -gq bids-validator@1.5.3
 
 # apt cleanup to recover as much space as possible
-RUN apt-get remove -y libegl1-mesa-dev && \
-    apt-get autoremove -y && \
+#RUN apt-get remove -y libegl1-mesa-dev && \
+RUN apt-get autoremove -y && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
@@ -95,30 +110,30 @@ RUN wget -q https://github.com/AlistairPerry/CCA/raw/master/parcellations/512inM
 #    rm -f oasis.zip
 RUN wget -qO- http://www.nitrc.org/frs/download.php/5906/ADHD200_parcellations.tar.gz | \
     tar zx -C /opt
-RUN wget -q "https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/5528816/lh.HCPMMP1.annot" \
-    -O /opt/freesurfer/subjects/fsaverage/label/lh.HCPMMP1.annot && \
-    wget -q "https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/5528819/rh.HCPMMP1.annot" \
-    -O /opt/freesurfer/subjects/fsaverage/label/rh.HCPMMP1.annot
-RUN mkdir /opt/brainnetome && \
-    ( wget -q "http://ddl.escience.cn/f/IiyU?func=download&rid=8135438" -O /opt/freesurfer/average/rh.BN_Atlas.gcs || \
-    wget -q "https://osf.io/e6zkg/download" -O /opt/freesurfer/average/rh.BN_Atlas.gcs ) && \
-    ( wget -q "http://ddl.escience.cn/f/IiyP?func=download&rid=8135433" -O /opt/freesurfer/average/lh.BN_Atlas.gcs || \
-    wget -q "https://osf.io/af9ut/download" -O /opt/freesurfer/average/lh.BN_Atlas.gcs ) && \
-    ( wget -q "http://ddl.escience.cn/f/PC7Q?func=download&rid=9882718" -O /opt/freesurfer/average/BN_Atlas_subcortex.gca || \
-    wget -q "https://osf.io/k2cd8/download" -O /opt/freesurfer/average/BN_Atlas_subcortex.gca ) && \
-    ( wget -q "http://ddl.escience.cn/f/PC7O?func=download&rid=9882716" -O /opt/brainnetome/BN_Atlas_246_LUT.txt || \
-    wget -q "https://osf.io/eb7pm/download" -O /opt/brainnetome/BN_Atlas_246_LUT.txt ) && \
-    ( wget -q "http://ddl.escience.cn/f/Bvhg?func=download&rid=6516020" -O /opt/brainnetome/BNA_MPM_thr25_1.25mm.nii.gz || \
-    wget -q "https://osf.io/dbqep/download" -O /opt/brainnetome/BNA_MPM_thr25_1.25mm.nii.gz ) && \
-    cp /opt/brainnetome/BN_Atlas_246_LUT.txt /opt/freesurfer/
-RUN wget -qO- "https://github.com/ThomasYeoLab/CBIG/archive/v0.11.1-Wu2017_RegistrationFusion.tar.gz" | \
-    tar zx -C /opt && \
-    cp /opt/CBIG-0.11.1-Wu2017_RegistrationFusion/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/*h.Yeo2011_*Networks_N1000.split_components.annot /opt/freesurfer/subjects/fsaverage5/label/ && \
-    cp /opt/CBIG-0.11.1-Wu2017_RegistrationFusion/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/project_to_individual/Yeo2011_*networks_Split_Components_LUT.txt /opt/freesurfer/ && \
-    mkdir /opt/Yeo2011 && \
-    cp /opt/CBIG-0.11.1-Wu2017_RegistrationFusion/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/Yeo2011_*Networks_N1000.split_components.FSL_MNI152_*mm.nii.gz /opt/Yeo2011/ && \
-    cp /opt/CBIG-0.11.1-Wu2017_RegistrationFusion/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/*Networks_ColorLUT_freeview.txt /opt/Yeo2011/ && \
-    rm -rf /opt/CBIG-0.11.1-Wu2017_RegistrationFusion
+#RUN wget -q "https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/5528816/lh.HCPMMP1.annot" \
+#    -O /opt/freesurfer/subjects/fsaverage/label/lh.HCPMMP1.annot && \
+#    wget -q "https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/5528819/rh.HCPMMP1.annot" \
+#    -O /opt/freesurfer/subjects/fsaverage/label/rh.HCPMMP1.annot
+#RUN mkdir /opt/brainnetome && \
+#    ( wget -q "http://ddl.escience.cn/f/IiyU?func=download&rid=8135438" -O /opt/freesurfer/average/rh.BN_Atlas.gcs || \
+#    wget -q "https://osf.io/e6zkg/download" -O /opt/freesurfer/average/rh.BN_Atlas.gcs ) && \
+#    ( wget -q "http://ddl.escience.cn/f/IiyP?func=download&rid=8135433" -O /opt/freesurfer/average/lh.BN_Atlas.gcs || \
+#    wget -q "https://osf.io/af9ut/download" -O /opt/freesurfer/average/lh.BN_Atlas.gcs ) && \
+#    ( wget -q "http://ddl.escience.cn/f/PC7Q?func=download&rid=9882718" -O /opt/freesurfer/average/BN_Atlas_subcortex.gca || \
+#    wget -q "https://osf.io/k2cd8/download" -O /opt/freesurfer/average/BN_Atlas_subcortex.gca ) && \
+#    ( wget -q "http://ddl.escience.cn/f/PC7O?func=download&rid=9882716" -O /opt/brainnetome/BN_Atlas_246_LUT.txt || \
+#    wget -q "https://osf.io/eb7pm/download" -O /opt/brainnetome/BN_Atlas_246_LUT.txt ) && \
+#    ( wget -q "http://ddl.escience.cn/f/Bvhg?func=download&rid=6516020" -O /opt/brainnetome/BNA_MPM_thr25_1.25mm.nii.gz || \
+#    wget -q "https://osf.io/dbqep/download" -O /opt/brainnetome/BNA_MPM_thr25_1.25mm.nii.gz ) && \
+#    cp /opt/brainnetome/BN_Atlas_246_LUT.txt /opt/freesurfer/
+#RUN wget -qO- "https://github.com/ThomasYeoLab/CBIG/archive/v0.11.1-Wu2017_RegistrationFusion.tar.gz" | \
+#    tar zx -C /opt && \
+#    cp /opt/CBIG-0.11.1-Wu2017_RegistrationFusion/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/*h.Yeo2011_*Networks_N1000.split_components.annot /opt/freesurfer/subjects/fsaverage5/label/ && \
+#    cp /opt/CBIG-0.11.1-Wu2017_RegistrationFusion/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/project_to_individual/Yeo2011_*networks_Split_Components_LUT.txt /opt/freesurfer/ && \
+#    mkdir /opt/Yeo2011 && \
+#    cp /opt/CBIG-0.11.1-Wu2017_RegistrationFusion/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/Yeo2011_*Networks_N1000.split_components.FSL_MNI152_*mm.nii.gz /opt/Yeo2011/ && \
+#    cp /opt/CBIG-0.11.1-Wu2017_RegistrationFusion/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/*Networks_ColorLUT_freeview.txt /opt/Yeo2011/ && \
+#    rm -rf /opt/CBIG-0.11.1-Wu2017_RegistrationFusion
 
 # Setup envvars
 ENV ANTSPATH=/usr/lib/ants \
@@ -146,14 +161,45 @@ ENV ANTSPATH=/usr/lib/ants \
 
 # MRtrix3 setup
 # Commitish is 3.0.2 plus relevant hotfix
-RUN git clone https://github.com/MRtrix3/mrtrix3.git /opt/mrtrix3 && \
-    cd /opt/mrtrix3 && \
-    git checkout 4ab54489f40997f7da1e1915c2adde3373cf6039 && \
-    python3 configure -nogui && \
-    python3 build -persistent -nopaginate && \
-    git describe --tags > /mrtrix3_version && \
-    rm -rf .git/ cmd/ core/ src/ testing/ tmp/ && \
-    cd /
+#RUN git clone https://github.com/MRtrix3/mrtrix3.git /opt/mrtrix3 && \
+#    cd /opt/mrtrix3 && \
+#    git checkout dev && \
+#    python3 configure -nogui && \
+#    python3 build -persistent -nopaginate && \
+#    git describe --tags > /mrtrix3_version && \
+#    rm -rf .git/ cmd/ core/ src/ testing/ tmp/ && \
+#    cd /
+
+FROM base-builder AS mrtrix3-builder
+
+# Git commitish from which to build MRtrix3.
+ARG MRTRIX3_GIT_COMMITISH="dev"
+# Command-line arguments for `./configure`
+ARG MRTRIX3_CONFIGURE_FLAGS=""
+# Command-line arguments for `./build`
+ARG MRTRIX3_BUILD_FLAGS="-persistent -nopaginate"
+
+RUN apt-get -qq update \
+    && apt-get install -yq --no-install-recommends \
+        libeigen3-dev \
+        libfftw3-dev \
+        libgl1-mesa-dev \
+        libpng-dev \
+        libqt5opengl5-dev \
+        libqt5svg5-dev \
+        libtiff5-dev \
+        qt5-default \
+        zlib1g-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Clone, build, and install MRtrix3.
+ARG MAKE_JOBS="1"
+#ARG MAKE_JOBS
+WORKDIR /opt/mrtrix3
+RUN git clone -b $MRTRIX3_GIT_COMMITISH --depth 1 https://github.com/MRtrix3/mrtrix3.git . \
+    && ./configure $MRTRIX3_CONFIGURE_FLAGS \
+    && NUMBER_OF_PROCESSORS=$MAKE_JOBS ./build $MRTRIX3_BUILD_FLAGS \
+    && rm -rf tmp
 
 # Acquire extra MRtrix3 data
 RUN wget -q "https://osf.io/v8n5g/download" -O /opt/mrtrix3/share/mrtrix3/labelconvert/Yeo2011_7N_split.txt && \

diff --git a/README.md b/README.md
@@ -9,6 +9,58 @@ normalisation.
 **NOTE**: App is still under development; script is not guaranteed to be operational
 for all use cases.
 
+## Changes relative to the original (this is a fork)
+
+We tried to adapt the code to incorporate synb0 processing, an approach described in:
+https://www.sciencedirect.com/science/article/pii/S0730725X18306179
+
+See also: https://github.com/BIDS-Apps/MRtrix3_connectome/issues/81
+
+First, you need to run synb0 (e.g. using https://github.com/treanus/KUL_NeuroImaging_Tools/blob/master/KUL_synb0.sh).
+This will use BIDS data is input, run synb0 with topup and store the relevant output in the BIDS derivatives as follows:
+
+    BIDS/derivatives/
+     └── synb0
+        ├── sub-iz01
+        │   ├── ses-01
+        │   │   └── topup
+        │   │       ├── topup_fieldcoef.nii.gz
+        │   │       └── topup_movpar.txt
+        │   └── ses-02
+        │       └── topup
+        │           ├── topup_fieldcoef.nii.gz
+        │           └── topup_movpar.txt
+        ├── sub-iz02
+        │   ├── ses-01
+        │   │   └── topup
+        │   │       ├── topup_fieldcoef.nii.gz
+        │   │       └── topup_movpar.txt
+        │   └── ses-02
+        │       └── topup
+        │           ├── topup_fieldcoef.nii.gz
+        │           └── topup_movpar.txt
+
+The above is then used as input to the mrtrix3_connectome.py command. 
+An new option was created:
++ **--topup_preproc prefix**<br>Provide a prefix by which pre-processed topup image data may be found for the processed participant(s) / session(s)
+
+Using 'mrtrix3_connectome.py bids_dir output_dir preproc [ options ] **-topup_preproc synb0**' means that the synb0 data in /BIDS/derivatives/synb0 will be used.
+
+Internally this works since the dwifslpreproc command of MRtrix3 dev branch (3.1) has a new option '-topup_files'. See https://github.com/MRtrix3/mrtrix3/blob/dev/bin/dwifslpreproc
+
+You thus need to have the dev branch of MRtrix3 installed:
+
+    git pull
+    git checkout dev
+    ./configure
+    ./build
+
+
+Note:
+For now this only works command line. There is no docker nor singularity container.
+
+
+
 ## Requirements
 
 Due to use of the Anatomically-Constrained Tractography (ACT) framework, correction of