diannepat/fsl6 repository overview

This is the full install of FSL 6.0.1 (with data, atlases, gui tools, cuda and gpu tools etc). It is based on https://github.com/BIDS-Apps/MRtrix3_connectome/blob/master/Dockerfile⁠

⁠Dockerfile:

FROM ubuntu:18.04
MAINTAINER Dianne Patterson [email protected]⁠

# Core system capabilities required.
# fslreorient2std needs bc
# /usr/local/fsl/bin/standard_space_roi needs dc
# flirt needs libopenblas-dev
RUN apt-get update && apt-get install -y
bc
dc
git
libopenblas-dev
nodejs
npm
python
tar
unzip
wget
&& apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN npm install -gq bids-validator

# Run FSL installer and remove unneeded directories
RUN wget -q http://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py⁠ && \
chmod 775 fslinstaller.py
RUN /fslinstaller.py -d /usr/local/fsl -q

# Make FSL happy
ENV FSLDIR=/usr/local/fsl
ENV PATH=$FSLDIR/bin:$PATH
RUN /bin/bash -c 'source /usr/local/fsl/etc/fslconf/fsl.sh'
ENV FSLMULTIFILEQUIT=TRUE
ENV FSLOUTPUTTYPE=NIFTI_GZ
RUN ln -s /usr/local/fsl/bin/eddy_openmp /usr/local/fsl/bin/eddy