diff --git a/Dockerfile b/Dockerfile index 12f642d..523ca47 100644 --- a/Dockerfile +++ b/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 bids-validator@1.8.4 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