Merge branch 'master' into dockerfix

Author: neurorepro

Dockerfile

@@ -1,7 +1,7 @@
 # Generated by Neurodocker and Reproenv.
 
 FROM neurodebian:bullseye
-ENV PATH="/opt/dcm2niix-v1.0.20211006/bin:$PATH"
+ENV PATH="/opt/dcm2niix-v1.0.20220720/bin:$PATH"
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
            ca-certificates \
@@ -16,10 +16,10 @@ RUN apt-get update -qq \
     && git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
     && cd /tmp/dcm2niix \
     && git fetch --tags \
-    && git checkout v1.0.20211006 \
+    && git checkout v1.0.20220720 \
     && mkdir /tmp/dcm2niix/build \
     && cd /tmp/dcm2niix/build \
-    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20211006 .. \
+    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 .. \
     && make -j1 \
     && make install \
     && rm -rf /tmp/dcm2niix
@@ -92,13 +92,13 @@ RUN printf '{ \
     { \
       "name": "env", \
       "kwds": { \
-        "PATH": "/opt/dcm2niix-v1.0.20211006/bin:$PATH" \
+        "PATH": "/opt/dcm2niix-v1.0.20220720/bin:$PATH" \
       } \
     }, \
     { \
       "name": "run", \
       "kwds": { \
-        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    ca-certificates \\\\\\n    cmake \\\\\\n    g++ \\\\\\n    gcc \\\\\\n    git \\\\\\n    make \\\\\\n    pigz \\\\\\n    zlib1g-dev\\nrm -rf /var/lib/apt/lists/*\\ngit clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix\\ncd /tmp/dcm2niix\\ngit fetch --tags\\ngit checkout v1.0.20211006\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20211006 ..\\nmake -j1\\nmake install\\nrm -rf /tmp/dcm2niix" \
+        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    ca-certificates \\\\\\n    cmake \\\\\\n    g++ \\\\\\n    gcc \\\\\\n    git \\\\\\n    make \\\\\\n    pigz \\\\\\n    zlib1g-dev\\nrm -rf /var/lib/apt/lists/*\\ngit clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix\\ncd /tmp/dcm2niix\\ngit fetch --tags\\ngit checkout v1.0.20220720\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 ..\\nmake -j1\\nmake install\\nrm -rf /tmp/dcm2niix" \
       } \
     }, \
     { \

utils/gen-docker-image.sh

@@ -8,11 +8,11 @@ VER=$(grep -Po '(?<=^__version__ = ).*' $thisd/../heudiconv/info.py | sed 's/"//
 image="kaczmarj/neurodocker:0.9.1"
 
 docker run --rm $image generate docker -b neurodebian:bullseye -p apt \
-    --dcm2niix version=v1.0.20211006 method=source \
+    --dcm2niix version=v1.0.20220720 method=source \
     --install git gcc pigz liblzma-dev libc-dev git-annex-standalone netbase \
     --copy . /src/heudiconv \
     --miniconda version="py39_4.12.0" conda_install="python=3.9 traits>=4.6.0 scipy numpy nomkl pandas" \
       pip_install="/src/heudiconv[all]" \
       pip_opts="--editable" \
     --entrypoint "heudiconv" \
-> ../Dockerfile
+> $thisd/../Dockerfile