finalize quickshear exampel

Author: vnm-neurodesk

.gitignore

@@ -21,4 +21,5 @@ recipes/fsl/fslinstaller.py
 .DS_Store
 .vscode/settings.json
 *.nii
+*.nii.gz
 *.h5

recipes/main_setup.sh

@@ -4,12 +4,26 @@
 #install neurodocker
 #pip install --no-cache-dir https://github.com/kaczmarj/neurodocker/tarball/master --user
 
-# install development version
-yes | pip uninstall neurodocker
-# python -m pip install --no-cache-dir https://github.com/ReproNim/neurodocker/tarball/master --upgrade
-#       For example, if you're using pip, instead of https://github.com/user/proj/archive/master.zip use git+https://github.com/user/proj.git#egg=proj
+# Parse command line arguments
+reinstall_neurodocker="true"  # default value
+for arg in "$@"
+do
+       case $arg in
+              --reinstall_neurodocker=*)
+              reinstall_neurodocker="${arg#*=}"
+              shift
+              ;;
+       esac
+done
 
-python -m pip install --no-cache-dir git+https://github.com/ReproNim/neurodocker.git#egg=neurodocker --upgrade
+# Check for reinstall_neurodocker parameter
+if [ "$reinstall_neurodocker" = "true" ]; then
+       # install development version
+       yes | pip uninstall neurodocker
+       # python -m pip install --no-cache-dir https://github.com/ReproNim/neurodocker/tarball/master --upgrade
+       #       For example, if you're using pip, instead of https://github.com/user/proj/archive/master.zip use git+https://github.com/user/proj.git#egg=proj
+       python -m pip install --no-cache-dir git+https://github.com/ReproNim/neurodocker.git#egg=neurodocker --upgrade
+fi
 
 
 export PATH=$PATH:~/.local/bin

recipes/quickshear/README.md

@@ -1,6 +1,6 @@
 
 ----------------------------------
-## quickshear/toolVersion ##
+## quickshear/1.1.0 ##
 Quickshear uses a skull stripped version of an anatomical image as a reference to deface the unaltered anatomical image.
 
 Example:
@@ -12,7 +12,7 @@ quickshear input.nii.gz mask.nii.gz defaced.nii.gz
 
 More documentation can be found here: [link_to_documentation](https://github.com/nipy/quickshear)
 
-To make the executables and scripts inside this container transparently available in the command line of environments where Neurocommand is installed: ml quickshear/toolVersion
+To make the executables and scripts inside this container transparently available in the command line of environments where Neurocommand is installed: ml quickshear/1.1.0
 
 Citation:
 ```

recipes/quickshear/build.sh

@@ -5,7 +5,10 @@ if [ "$1" != "" ]; then
     echo "Entering Debug mode"
     export debug=$1
 fi
-source ../main_setup.sh
+
+source ../main_setup.sh --reinstall_neurodocker=false
+
+# freesurfer/synthstrip:1.6 = Ubuntu Jammy 22.04
 
 neurodocker generate ${neurodocker_buildMode} \
    --base-image freesurfer/synthstrip:1.6 \
@@ -17,6 +20,28 @@ neurodocker generate ${neurodocker_buildMode} \
    --workdir /opt \
    --install wget git curl ca-certificates python3 python3-pip \
    --run="pip install quickshear==1.2.0" \
+   --install build-essential libxslt1.1 libhdf5-103 libboost-program-options1.74.0 libpugixml1v5 vim dos2unix git cmake g++ libhdf5-dev libxml2-dev libxslt1-dev libboost-all-dev libfftw3-dev libpugixml-dev \
+   --workdir='/opt/code' \
+   --run='git clone https://github.com/ismrmrd/ismrmrd.git && \
+      cd ./ismrmrd && \
+      cmake . && \
+      make -j $(nproc) && \
+      make install' \
+   --run='git clone https://github.com/ismrmrd/siemens_to_ismrmrd.git && \
+      cd siemens_to_ismrmrd && \
+      mkdir build && \
+      cd build && \
+      cmake .. && \
+      make -j $(nproc) && \
+      make install' \
+   --run='pip3 install h5py ismrmrd matplotlib pydicom pynetdicom nibabel' \
+   --run='git clone https://github.com/ismrmrd/ismrmrd-python-tools.git && \
+      cd ismrmrd-python-tools && \
+      pip3 install --no-cache-dir .' \
+   --run='git clone https://github.com/kspaceKelvin/python-ismrmrd-server && \
+      find /opt/code/python-ismrmrd-server -name "*.sh" -exec chmod +x {} \; && \
+      find /opt/code/python-ismrmrd-server -name "*.sh" | xargs dos2unix' \
+   --copy invertcontrast.py /opt/code/python-ismrmrd-server/invertcontrast.py \
    --env DEPLOY_BINS=mri_synthstrip:quickshear \
    --copy README.md /README.md \
    --entrypoint bash \