From b52a37cf780763e3278dddc000958e46abdf10f9 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 14 Oct 2024 17:43:19 -0400
Subject: [PATCH 1/3] Docker image: Use newer debian stable for the base and
 newer dcm2niix

---
 utils/gen-docker-image.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/utils/gen-docker-image.sh b/utils/gen-docker-image.sh
index aeb598b4..e4ceecda 100755
--- a/utils/gen-docker-image.sh
+++ b/utils/gen-docker-image.sh
@@ -8,10 +8,10 @@ VER=$(grep -Po '(?<=^__version__ = ).*' $thisd/../heudiconv/info.py | sed 's/"//
 image="kaczmarj/neurodocker:0.9.1"
 
 docker run --rm $image generate docker \
-    --base-image neurodebian:bullseye \
+    --base-image neurodebian:bookworm \
     --pkg-manager apt \
     --dcm2niix \
-        version=v1.0.20220720 \
+        version=v1.0.20240202 \
         method=source \
         cmake_opts="-DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON" \
     --install \

From aaabcb0314e994ed709c8d2c0532032601ebf257 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 14 Oct 2024 17:45:37 -0400
Subject: [PATCH 2/3] Make it possible to use podman or docker

---
 utils/gen-docker-image.sh | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/utils/gen-docker-image.sh b/utils/gen-docker-image.sh
index e4ceecda..efa149c9 100755
--- a/utils/gen-docker-image.sh
+++ b/utils/gen-docker-image.sh
@@ -7,7 +7,16 @@ VER=$(grep -Po '(?<=^__version__ = ).*' $thisd/../heudiconv/info.py | sed 's/"//
 
 image="kaczmarj/neurodocker:0.9.1"
 
-docker run --rm $image generate docker \
+if hash podman; then
+    OCI_BINARY=podman
+elif hash docker; then
+    OCI_BINARY=docker
+else
+    echo "ERROR: no podman or docker found" >&2
+    exit 1
+fi
+
+${OCI_BINARY:-docker} run --rm $image generate docker \
     --base-image neurodebian:bookworm \
     --pkg-manager apt \
     --dcm2niix \

From 06649a6686b25708ca6071744f061a976b309988 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 14 Oct 2024 17:47:15 -0400
Subject: [PATCH 3/3] updated Dockerfile

---
 Dockerfile | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index f9bf7fd2..062756f9 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,7 +1,7 @@
 # Generated by Neurodocker and Reproenv.
 
-FROM neurodebian:bullseye
-ENV PATH="/opt/dcm2niix-v1.0.20220720/bin:$PATH"
+FROM neurodebian:bookworm
+ENV PATH="/opt/dcm2niix-v1.0.20240202/bin:$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 v1.0.20220720 \
+    && git checkout v1.0.20240202 \
     && mkdir /tmp/dcm2niix/build \
     && cd /tmp/dcm2niix/build \
-    && cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 .. \
+    && cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20240202 .. \
     && make -j1 \
     && make install \
     && rm -rf /tmp/dcm2niix
@@ -87,19 +87,19 @@ RUN printf '{ \
     { \
       "name": "from_", \
       "kwds": { \
-        "base_image": "neurodebian:bullseye" \
+        "base_image": "neurodebian:bookworm" \
       } \
     }, \
     { \
       "name": "env", \
       "kwds": { \
-        "PATH": "/opt/dcm2niix-v1.0.20220720/bin:$PATH" \
+        "PATH": "/opt/dcm2niix-v1.0.20240202/bin:$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 v1.0.20220720\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 ..\\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 v1.0.20240202\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20240202 ..\\nmake -j1\\nmake install\\nrm -rf /tmp/dcm2niix" \
       } \
     }, \
     { \