Dockerfile - use bullseye for the base and fresh dcm2niix

Author: yarikoptic

Dockerfile

@@ -1,13 +1,13 @@
 # Generated by Neurodocker version 0.4.2-3-gf7055a1
-# Timestamp: 2022-04-04 17:55:39 UTC
+# Timestamp: 2022-04-06 17:10:29 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
 # pull request on our GitHub repository:
 # 
 #     https://github.com/kaczmarj/neurodocker
 
-FROM neurodebian:stretch
+FROM neurodebian:bullseye
 
 ARG DEBIAN_FRONTEND="noninteractive"
 
@@ -39,7 +39,7 @@ RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
 
 ENTRYPOINT ["/neurodocker/startup.sh"]
 
-ENV PATH="/opt/dcm2niix-v1.0.20190410/bin:$PATH"
+ENV PATH="/opt/dcm2niix-v1.0.20211006/bin:$PATH"
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
            cmake \
@@ -54,10 +54,10 @@ RUN apt-get update -qq \
     && git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
     && cd /tmp/dcm2niix \
     && git fetch --tags \
-    && git checkout v1.0.20190410 \
+    && git checkout v1.0.20211006 \
     && mkdir /tmp/dcm2niix/build \
     && cd /tmp/dcm2niix/build \
-    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20190410 .. \
+    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20211006 .. \
     && make \
     && make install \
     && rm -rf /tmp/dcm2niix
@@ -110,12 +110,12 @@ RUN echo '{ \
     \n  "instructions": [ \
     \n    [ \
     \n      "base", \
-    \n      "neurodebian:stretch" \
+    \n      "neurodebian:bullseye" \
     \n    ], \
     \n    [ \
     \n      "dcm2niix", \
     \n      { \
-    \n        "version": "v1.0.20190410", \
+    \n        "version": "v1.0.20211006", \
     \n        "method": "source" \
     \n      } \
     \n    ], \

utils/gen-docker-image.sh

@@ -6,8 +6,8 @@ VER=$(grep -Po '(?<=^__version__ = ).*' ../heudiconv/info.py | sed 's/"//g')
 
 image="kaczmarj/neurodocker:master@sha256:936401fe8f677e0d294f688f352cbb643c9693f8de371475de1d593650e42a66"
 
-docker run --rm $image generate docker -b neurodebian:stretch -p apt \
-    --dcm2niix version=v1.0.20190410 method=source \
+docker run --rm $image generate docker -b neurodebian:bullseye -p apt \
+    --dcm2niix version=v1.0.20211006 method=source \
     --install git gcc pigz liblzma-dev libc-dev git-annex-standalone netbase \
     --copy . /src/heudiconv \
     --miniconda use_env=base conda_install="python=3.7 traits>=4.6.0 scipy numpy nomkl pandas" \