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Install FSL from old ASLPrep version. (#5)
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@@ -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 | ||
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@@ -130,6 +131,12 @@ ENV AFNI_MODELPATH="/usr/lib/afni/models" \ | |
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ENV PATH="/usr/lib/afni/bin:$PATH" | ||
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# Install FSL from old ASLPrep version | ||
COPY --from=build_fsl /opt/fsl-6.0.5/ /opt/fsl-6.0.5/ | ||
ENV FSLDIR="/opt/fsl-6.0.5" \ | ||
PATH="/opt/fsl-6.0.5/bin:$PATH" \ | ||
FSLOUTPUTTYPE="NIFTI_GZ" | ||
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# 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' \ | ||
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@@ -186,18 +193,6 @@ RUN npm install -g [email protected] | |
ENV MKL_NUM_THREADS=1 \ | ||
OMP_NUM_THREADS=1 | ||
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# 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" | ||
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# Create a shared $HOME directory | ||
RUN useradd -m -s /bin/bash -G users aslprep | ||
WORKDIR /home/aslprep | ||
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