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#%Module#
#
# FSL 5.0
#
# Ported to Environment Modules by Alex Waite <Alexqw85@gmail.com>
# Derived from the modified fsl.sh for Debian by Michael Hanke <michael.hanke@gmail.com>
# Original fsl.sh written by Mark Jenkinson, FMRIB Analysis Group, University of Oxford
## Short description of package:
module-whatis "FSL is a comprehensive library of image analysis and statistical tools for fMRI, MRI, and DTI brain imaging data."
## URL of application homepage:
set appurl http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
proc ModulesHelp { } {
puts stderr "Sets up the paths and environment variables for FSL 5.0."
}
## Local variables
set root_share /usr/share/fsl/5.0/
set root_lib /usr/lib/fsl/5.0/
## Environment variables
# Debian has a fixed FSLDIR
setenv FSLDIR $root_share
# Possum is installed in the same directory
setenv POSSUMDIR $root_share
# add the fsl binary path to the search path
prepend-path PATH $root_lib
# Configure the linker search path for Debian FSLs internal shared libraries
prepend-path LD_LIBRARY_PATH $root_lib
# The following variable selects the default output image type
# Legal values are:
# NIFTI, NIFTI_PAIR, NIFTI_GZ, NIFTI_PAIR_GZ
# This would typically be overwritten in by a script
# or in ${HOME}/privatemodules/ if the user wished to write files with
# a different format
setenv FSLOUTPUTTYPE NIFTI_GZ
# Comment out the definition of FSLMULTIFILEQUIT to enable
# FSL programs to soldier on after detecting multiple image
# files with the same basename ( e.g. epi.hdr and epi.nii )
setenv FSLMULTIFILEQUIT TRUE
# The following variables specify paths for programs and can be changed
# or replaced by different programs, by default set sensible Debian-defaults
setenv FSLTCLSH /usr/bin/tclsh
setenv FSLWISH /usr/bin/wish
setenv FSLBROWSER /etc/alternatives/x-www-browser
# The following variables are used for running code in parallel across
# several machines ( i.e. for FDT )
# for a cluster engine setup see below
setenv FSLLOCKDIR ''
setenv FSLMACHINELIST ''
setenv FSLREMOTECALL ''
# If set, tell FSL to use Sun Gridengine to submit jobs instead of running them
# directly on the machine. If unset, no attempt will be made to utilize
# gridengine, even if it is running. By default SGE is not utilized.
#setenv FSLPARALLEL 1
# Mail setup for gridengine jobs. See man qsub (-m option) for all possible
# settings. By default no email is sent.
setenv FSLCLUSTER_MAILOPTS "n"
# default queue for job submissions
#setenv FSLCLUSTER_DEFAULT_QUEUE "all.q"
# Warn if user has a legacy fsl.sh config that we won't be reading.
set legacy_user_conf $env(HOME)/.fslconf/fsl.sh
if { [ file exists "$legacy_user_conf" ] } {
puts stderr "\n#######################################################"
puts stderr "# Legacy $legacy_user_conf config file detected!"
puts stderr "# - Modules cannot parse this config file; it will be ignored."
puts stderr "# - If you need to override default values, either overwrite"
puts stderr "# - them in your shell now or write a privatemodule to load this"
puts stderr "# - module and `setenv` over the offending variables."
puts stderr "#######################################################\n"
puts stderr "FSL loaded successfully."
}
## EOB
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