From a8cb9c1bbd5b92542579485fd03b8ce371728924 Mon Sep 17 00:00:00 2001
From: arnaudbore <arnaud.bore@gmail.com>
Date: Tue, 19 Nov 2024 19:31:53 -0500
Subject: [PATCH 1/2] update dockerfile without slim and eddyqc fix

---
 Dockerfile | 28 ++++++++++++++++------------
 1 file changed, 16 insertions(+), 12 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 0a30e90d9f..008fa04cab 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,8 +1,8 @@
 ARG MAKE_JOBS="1"
 ARG DEBIAN_FRONTEND="noninteractive"
 
-FROM python:3.8-slim AS base
-FROM buildpack-deps:buster AS base-builder
+FROM python:3.8 AS base
+FROM buildpack-deps:bookworm AS base-builder
 
 FROM base-builder AS mrtrix3-builder
 
@@ -22,7 +22,8 @@ RUN apt-get -qq update \
         libqt5opengl5-dev \
         libqt5svg5-dev \
         libtiff5-dev \
-        qt5-default \
+        python3 \
+        qtbase5-dev \
         zlib1g-dev \
     && rm -rf /var/lib/apt/lists/*
 
@@ -30,8 +31,8 @@ RUN apt-get -qq update \
 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 \
+    && python3 ./configure $MRTRIX3_CONFIGURE_FLAGS \
+    && NUMBER_OF_PROCESSORS=$MAKE_JOBS python3 ./build $MRTRIX3_BUILD_FLAGS \
     && rm -rf tmp
 
 # Download minified ART ACPCdetect (V2.0).
@@ -51,10 +52,10 @@ FROM base-builder as freesurfer-installer
 WORKDIR /opt/freesurfer
 RUN curl -fsSLO https://raw.githubusercontent.com/freesurfer/freesurfer/v7.1.1/distribution/FreeSurferColorLUT.txt
 
-# Download minified FSL (6.0.4-2)
+# Download minified FSL (6.0.7.7)
 FROM base-builder as fsl-installer
 WORKDIR /opt/fsl
-RUN curl -fsSL https://osf.io/dtep4/download \
+RUN curl -fsSL https://osf.io/ph9ex/download \
     | tar xz --strip-components 1
 
 # Build final image.
@@ -66,7 +67,8 @@ RUN apt-get -qq update \
         binutils \
         dc \
         less \
-        libfftw3-3 \
+        libfftw3-single3 \
+        libfftw3-double3 \
         libgl1-mesa-glx \
         libgomp1 \
         liblapack3 \
@@ -77,7 +79,8 @@ RUN apt-get -qq update \
         libqt5svg5 \
         libqt5widgets5 \
         libquadmath0 \
-        libtiff5 \
+        libtiff5-dev \
+        python3 \
         python3-distutils \
     && rm -rf /var/lib/apt/lists/*
 
@@ -95,12 +98,13 @@ ENV ANTSPATH="/opt/ants/bin" \
     FSLMULTIFILEQUIT="TRUE" \
     FSLTCLSH="/opt/fsl/bin/fsltclsh" \
     FSLWISH="/opt/fsl/bin/fslwish" \
-    LD_LIBRARY_PATH="/opt/fsl/lib:$LD_LIBRARY_PATH" \
-    PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/bin:$PATH"
+    PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/share/fsl/bin:$PATH"
 
 # Fix "Singularity container cannot load libQt5Core.so.5" on CentOS 7
 RUN strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5 \
     && ldconfig \
     && apt-get purge -yq binutils
 
-CMD ["/bin/bash"]
+RUN ln -s /usr/bin/python3 /usr/bin/python
+
+CMD ["/bin/bash"]
\ No newline at end of file

From 6249ad275e7b6accc9d203be84ce446b50e40733 Mon Sep 17 00:00:00 2001
From: arnaudbore <arnaud.bore@gmail.com>
Date: Wed, 20 Nov 2024 23:13:15 -0500
Subject: [PATCH 2/2] restore slim version and add procps

---
 Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 008fa04cab..ef7d6a9a6f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,7 +1,7 @@
 ARG MAKE_JOBS="1"
 ARG DEBIAN_FRONTEND="noninteractive"
 
-FROM python:3.8 AS base
+FROM python:3.8-slim AS base
 FROM buildpack-deps:bookworm AS base-builder
 
 FROM base-builder AS mrtrix3-builder
@@ -82,6 +82,7 @@ RUN apt-get -qq update \
         libtiff5-dev \
         python3 \
         python3-distutils \
+        procps \
     && rm -rf /var/lib/apt/lists/*
 
 COPY --from=acpcdetect-installer /opt/art /opt/art