maint: install fsl and convert3D from conda

Author: eilidhmacnicol

Dockerfile

@@ -33,8 +33,7 @@ RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/frees
     | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer-exclude.txt
 
 # Simulate SetUpFreeSurfer.sh
-ENV FSL_DIR="/opt/fsl-5.0.11" \
-    OS="Linux" \
+ENV OS="Linux" \
     FS_OVERRIDE=0 \
     FIX_VERTEX_AREA="" \
     FSF_OUTPUT_FORMAT="nii.gz" \
@@ -50,98 +49,6 @@ ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
     MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
     PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
 
-# FSL 5.0.11 (neurodocker build)
-RUN apt-get update -qq \
-    && apt-get install -y -q --no-install-recommends \
-           bc \
-           dc \
-           file \
-           libfontconfig1 \
-           libfreetype6 \
-           libgl1-mesa-dev \
-           libgl1-mesa-dri \
-           libglu1-mesa-dev \
-           libgomp1 \
-           libice6 \
-           libxcursor1 \
-           libxft2 \
-           libxinerama1 \
-           libxrandr2 \
-           libxrender1 \
-           libxt6 \
-           sudo \
-           wget \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && echo "Downloading FSL ..." \
-    && mkdir -p /opt/fsl-5.0.11 \
-    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-centos6_64.tar.gz \
-    | tar -xz -C /opt/fsl-5.0.11 --strip-components 1 \
-    --exclude "fsl/config" \
-    --exclude "fsl/data/atlases" \
-    --exclude "fsl/data/first" \
-    --exclude "fsl/data/mist" \
-    --exclude "fsl/data/possum" \
-    --exclude "fsl/data/standard/bianca" \
-    --exclude "fsl/data/standard/tissuepriors" \
-    --exclude "fsl/doc" \
-    --exclude "fsl/etc/default_flobs.flobs" \
-    --exclude "fsl/etc/fslconf" \
-    --exclude "fsl/etc/js" \
-    --exclude "fsl/etc/luts" \
-    --exclude "fsl/etc/matlab" \
-    --exclude "fsl/extras" \
-    --exclude "fsl/include" \
-    --exclude "fsl/python" \
-    --exclude "fsl/refdoc" \
-    --exclude "fsl/src" \
-    --exclude "fsl/tcl" \
-    --exclude "fsl/bin/FSLeyes" \
-    && find /opt/fsl-5.0.11/bin -type f -not \( \
-        -name "applywarp" -or \
-        -name "bet" -or \
-        -name "bet2" -or \
-        -name "convert_xfm" -or \
-        -name "fast" -or \
-        -name "flirt" -or \
-        -name "fsl_regfilt" -or \
-        -name "fslhd" -or \
-        -name "fslinfo" -or \
-        -name "fslmaths" -or \
-        -name "fslmerge" -or \
-        -name "fslroi" -or \
-        -name "fslsplit" -or \
-        -name "fslstats" -or \
-        -name "imtest" -or \
-        -name "mcflirt" -or \
-        -name "melodic" -or \
-        -name "prelude" -or \
-        -name "remove_ext" -or \
-        -name "susan" -or \
-        -name "topup" -or \
-        -name "zeropad" \) -delete \
-    && find /opt/fsl-5.0.11/data/standard -type f -not -name "MNI152_T1_2mm_brain.nii.gz" -delete
-ENV FSLDIR="/opt/fsl-5.0.11" \
-    PATH="/opt/fsl-5.0.11/bin:$PATH" \
-    FSLOUTPUTTYPE="NIFTI_GZ" \
-    FSLMULTIFILEQUIT="TRUE" \
-    FSLLOCKDIR="" \
-    FSLMACHINELIST="" \
-    FSLREMOTECALL="" \
-    FSLGECUDAQ="cuda.q" \
-    LD_LIBRARY_PATH="/opt/fsl-5.0.11/lib:$LD_LIBRARY_PATH"
-
-# Convert3D (neurodocker build)
-RUN echo "Downloading Convert3D ..." \
-    && mkdir -p /opt/convert3d-1.0.0 \
-    && curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download \
-    | tar -xz -C /opt/convert3d-1.0.0 --strip-components 1 \
-    --exclude "c3d-1.0.0-Linux-x86_64/lib" \
-    --exclude "c3d-1.0.0-Linux-x86_64/share" \
-    --exclude "c3d-1.0.0-Linux-x86_64/bin/c3d_gui"
-ENV C3DPATH="/opt/convert3d-1.0.0" \
-    PATH="/opt/convert3d-1.0.0/bin:$PATH"
-
 # AFNI latest (neurodocker build)
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
@@ -212,7 +119,35 @@ ENV PATH="/opt/conda/bin:$PATH" \
     LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH" \
     LANG="C.UTF-8" \
     LC_ALL="C.UTF-8" \
-    PYTHONNOUSERSITE=1
+    PYTHONNOUSERSITE=1 \
+    FSLDIR="/opt/conda" \
+    FSLOUTPUTTYPE="NIFTI_GZ" \
+    FSLMULTIFILEQUIT="TRUE" \
+    FSLLOCKDIR="" \
+    FSLMACHINELIST="" \
+    FSLREMOTECALL="" \
+    FSLGECUDAQ="cuda.q"
+
+# Install FSL and Convert3D from conda packages
+# Specific FSL pins are derived from
+# https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.6.2_linux-64.yml
+RUN conda install -y -n base \
+    -c anaconda \
+    -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ \
+    -c conda-forge \
+    convert3d=1.3.0 \
+    fsl-flirt=2111.0 \
+    fsl-fast4=2111.0 \
+    fsl-fugue=2201.2 \
+    fsl-mcflirt=2111.0 \
+    fsl-melodic=2111.1 \
+    fsl-miscmaths=2203.2 \
+    fsl-topup=2203.1 \
+    fsl-susan=2111.0 \
+    && sync \
+    && conda clean -afy; sync \
+    && rm -rf ~/.conda ~/.cache/pip/*; sync \
+    && ldconfig
 
 # Unless otherwise specified each process should only use one thread - nipype
 # will handle parallelization