diff --git a/Dockerfile b/Dockerfile index b78e120..1dfd12c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -172,6 +172,20 @@ RUN apt-get update -qq \ fi \ && ldconfig +# Install FSL from old ASLPrep version +# Based on https://github.com/ReproNim/neurodocker/blob/a87693e5676e7c4d272bc4eb8285f9232860d0ff/neurodocker/templates/fsl.yaml +RUN curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python3 - -d /opt/fsl-6.0.7.1 -V 6.0.7.1 +ENV FSLDIR="/opt/fsl-6.0.7.1" \ + PATH="$PATH:/opt/fsl-6.0.7.1/bin" \ + FSLOUTPUTTYPE="NIFTI_GZ" \ + FSLMULTIFILEQUIT="TRUE" \ + FSLTCLSH="/opt/fsl-6.0.7.1/bin/fsltclsh" \ + FSLWISH="/opt/fsl-6.0.7.1/bin/fslwish" \ + FSLLOCKDIR="" \ + FSLMACHINELIST="" \ + FSLREMOTECALL="" \ + FSLGECUDAQ="cuda.q" + # Install files from stages COPY --from=freesurfer /opt/freesurfer /opt/freesurfer COPY --from=afni /opt/afni-latest /opt/afni-latest diff --git a/env.yml b/env.yml index caeaaa4..0f92f7a 100644 --- a/env.yml +++ b/env.yml @@ -1,6 +1,5 @@ name: aslprep channels: - - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ - conda-forge # Update this ~yearly; last updated Jan 2024 dependencies: @@ -27,15 +26,6 @@ dependencies: - pandoc=3.1 # Workflow dependencies: ANTs - ants=2.5 - # Workflow dependencies: FSL (versions pinned in 6.0.7.7) - - fsl-bet2=2111.4 - - fsl-flirt=2111.2 - - fsl-fast4=2111.3 - - fsl-fugue=2201.4 - - fsl-mcflirt=2111.0 - - fsl-miscmaths=2203.2 - - fsl-oxford_asl=v4.0.28 - - fsl-topup=2203.2 - pip variables: FSLOUTPUTTYPE: NIFTI_GZ