FSL installation for Fish shell

README.md

1. Install FSL using a compatible shell (bash or tcsh), using the usual method.
2. Copy fsl.fish to the appropriate location (usually /usr/local/fsl/etc/fslconf/).
3. Append the contents of config.fish to your own config.fish

config.fish

# fsl
set -x FSLDIR /usr/local/fsl
source $FSLDIR/etc/fslconf/fsl.fish
set -gx PATH $FSLDIR/bin $PATH

fsl.fish

#### Set up standard FSL user environment variables ####

# The following variable selects the default output image type
# Legal values are:  ANALYZE  NIFTI  NIFTI_PAIR  ANALYZE_GZ  NIFTI_GZ  NIFTI_PAIR_GZ
# This would typically be overwritten in ${HOME}/.fslconf/fsl.sh if the user wished
#  to write files with a different format
set -x 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 )
set -x FSLMULTIFILEQUIT True


# The following variables specify paths for programs and can be changed
#  or replaced by different programs ( e.g. FSLDISPLAY=open   for MacOSX)

set -x FSLTCLSH $FSLDIR/bin/fsltclsh
set -x FSLWISH $FSLDIR/bin/fslwish
set -x FSLDISPLAY open

# The following variables are used to configure CUDA capable queues - if you
# are using Grid Engine then this queue will be used to enqueue tasks that
# support execution on NVIDIA CUDA hardware.
set -x FSLGECUDAQ "cuda.q"

# Set up development variables (not for the faint-hearted)
# Uncomment the following if you wish to compile FSL source code
#FSLCONFDIR=$FSLDIR/config
#FSLMACHTYPE=`$FSLDIR/etc/fslconf/fslmachtype.sh`

#set -x FSLCONFDIR FSLMACHTYPE


###################################################
### Add other global environment variables here ###
###      or change the definitions above        ###
###################################################


# USER VARIABLES HERE