pndni/minc-ants-fsl-and-fs-container:1.1.0

$ singularity pull shub://pndni/minc-ants-fsl-and-fs-container:1.1.0

Singularity Recipe

Bootstrap: shub
From: pndni/minc-ants-and-fsl-container:1.1.0
# OSVersion: 7
# MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/x86_64/
# Include: yum
#
%post

    ##############
    # freesurfer #
    ##############
    wget --no-verbose --output-document=/root/freesurfer.tar.gz 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 -C /opt -xzvf /root/freesurfer.tar.gz
    rm /root/freesurfer.tar.gz

%appenv freesurfer
    if [ -n "$FSLDIR" ]
    then
	>&2 echo "freesurfer must be loaded before fsl"
	exit 1
    fi
    export NO_FSFAST=1
    export FREESURFER_HOME=/opt/freesurfer
    source $FREESURFER_HOME/SetUpFreeSurfer.sh

%applabels freesurfer
    License https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
    URL https://surfer.nmr.mgh.harvard.edu/
    Version 6.0.1

%apphelp freesurfer
    Using freesurfer requires a freesurfer license file.
    A license file may be obtained from
    https://surfer.nmr.mgh.harvard.edu/registration.html
    Ensure that the license file is visible from the container,
    and set the environment variable FS_LICENSE to point to it
    (or copy the file to /opt/freesurfer/license.txt from
    inside the container)

%appenv freesurfer_nominc
    export NO_MINC=1
    source $SCIF_APPENV_freesurfer

%labels
    Maintainer Steven Tilley
    Version 1.1.0

Collection

• Name: pndni/minc-ants-fsl-and-fs-container
• License: GNU General Public License v3.0

Metrics

Feedback

Was this page helpful?

Glad to hear it! Please tell us how we can improve.

Sorry to hear that. Please tell us how we can improve.