Install FSL from old ASLPrep version. (#5)

Dockerfile

@@ -1,3 +1,4 @@
+FROM pennlinc/aslprep:0.4.0 as build_fsl
 FROM pennlinc/atlaspack:0.0.4 as atlaspack
 FROM ubuntu:bionic-20220531
 
@@ -130,6 +131,12 @@ ENV AFNI_MODELPATH="/usr/lib/afni/models" \
 
 ENV PATH="/usr/lib/afni/bin:$PATH"
 
+# Install FSL from old ASLPrep version
+COPY --from=build_fsl /opt/fsl-6.0.5/ /opt/fsl-6.0.5/
+ENV FSLDIR="/opt/fsl-6.0.5" \
+    PATH="/opt/fsl-6.0.5/bin:$PATH" \
+    FSLOUTPUTTYPE="NIFTI_GZ"
+
 # Install FreeSurfer
 RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
     --exclude='freesurfer/diffusion' \
@@ -186,18 +193,6 @@ RUN npm install -g [email protected]
 ENV MKL_NUM_THREADS=1 \
     OMP_NUM_THREADS=1
 
-# FSL environment
-ENV LANG="C.UTF-8" \
-    LC_ALL="C.UTF-8" \
-    PYTHONNOUSERSITE=1 \
-    FSLDIR="/usr/local/miniconda" \
-    FSLOUTPUTTYPE="NIFTI_GZ" \
-    FSLMULTIFILEQUIT="TRUE" \
-    FSLLOCKDIR="" \
-    FSLMACHINELIST="" \
-    FSLREMOTECALL="" \
-    FSLGECUDAQ="cuda.q"
-
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users aslprep
 WORKDIR /home/aslprep