Thanks everybody for your help! I'm
obviously clueless and still haven't gotten it
fixed despite all your help, but I've got some
more insight:
If I type
export
in my bash terminal window, I get the following
output:
declare -x
Apple_PubSub_Socket_Render="/tmp/launch-3gf3KZ/Render"
declare -x
Apple_Ubiquity_Message="/tmp/launch-lLg0UN/Apple_Ubiquity_Message"
declare -x COMMAND_MODE="unix2003"
declare -x
DISPLAY="/tmp/launch-4z6zzb/org.macosforge.xquartz:0"
declare -x FSLCONFDIR="/usr/local/fsl/config"
declare -x FSLDIR="/usr/local/fsl"
declare -x FSLLOCKDIR=""
declare -x FSLMACHINELIST=""
declare -x FSLMACHTYPE=""
declare -x FSLMULTIFILEQUIT="TRUE"
declare -x FSLOUTPUTTYPE="NIFTI_GZ"
declare -x FSLREMOTECALL=""
declare -x FSLTCLSH="/usr/local/fsl/bin/fsltclsh"
declare -x FSLWISH="/usr/local/fsl/bin/fslwish"
declare -x HOME="/Users/anna"
declare -x LOGNAME="anna"
declare -x OLDPWD="/Users"
declare -x
PATH="/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/opt/X11/bin"
declare -x PWD="/"
declare -x SECURITYSESSIONID="186a4"
declare -x SHELL="/bin/bash"
declare -x SHLVL="2"
declare -x
SSH_AUTH_SOCK="/tmp/launch-unTD3D/Listeners"
declare -x TERM="xterm"
declare -x
TMPDIR="/var/folders/23/jbv5t1x52bq2rm6yc6xhjtvw0000gp/T/"
declare -x USER="annagreenwald"
declare -x WINDOWID="6291469"
declare -x
X11_PREFS_DOMAIN="org.macosforge.xquartz.X11"
declare -x XTERM_LOCALE="C"
declare -x XTERM_SHELL="/bin/bash"
declare -x XTERM_VERSION="XTerm(281)"
declare -x __CF_USER_TEXT_ENCODING="0x1F6:0:0"
Clearly, the fsldir is part of the PATH and
FSLOUTPUTTYPE is set.
In contrast, if I type
system('export')
into Matlab, I get
declare -x ARCH="maci64"
declare -x AUTOMOUNT_MAP=""
declare -x
Apple_PubSub_Socket_Render="/tmp/launch-3gf3KZ/Render"
declare -x
Apple_Ubiquity_Message="/tmp/launch-lLg0UN/Apple_Ubiquity_Message"
declare -x BASEMATLABPATH=""
declare -x COMMAND_MODE="unix2003"
declare -x
DISPLAY="/tmp/launch-4z6zzb/org.macosforge.xquartz:0"
declare -x
DYLD_FRAMEWORK_PATH="/Applications/MATLAB_R2013a.app/sys/os/maci64:/Applications/MATLAB_R2013a.app/bin/maci64/../../Contents/MacOS:/Applications/MATLAB_R2013a.app/bin/maci64:/Applications/MATLAB_R2013a.app/extern/lib/maci64:/Applications/MATLAB_R2013a.app/runtime/maci64"
declare -x
DYLD_LIBRARY_PATH="/Applications/MATLAB_R2013a.app/sys/os/maci64:/Applications/MATLAB_R2013a.app/bin/maci64/../../Contents/MacOS:/Applications/MATLAB_R2013a.app/bin/maci64:/Applications/MATLAB_R2013a.app/extern/lib/maci64:/Applications/MATLAB_R2013a.app/runtime/maci64"
declare -x FSLDIR="/usr/local/fsl"
declare -x GFORTRAN_STDERR_UNIT="-1"
declare -x GFORTRAN_STDIN_UNIT="-1"
declare -x GFORTRAN_STDOUT_UNIT="-1"
declare -x HOME="/Users/anna"
declare -x LANG="en_US.ISO8859-1"
declare -x LC_CTYPE="en_US.ISO8859-1"
declare -x LC_NUMERIC="C"
declare -x LOGNAME="anna"
declare -x MATLAB_USE_USERWORK=""
declare -x OLDPWD
declare -x
OSG_LD_LIBRARY_PATH="/Applications/MATLAB_R2013a.app/sys/openscenegraph/lib/maci64"
declare -x PATH="/usr/bin:/bin:/usr/sbin:/sbin"
declare -x PWD="/"
declare -x SHELL="/bin/bash"
declare -x SHLVL="1"
declare -x SSH_AUTH_SOCK="/tmp/launch-unTD3D/Listeners"
declare -x TERM="dumb"
declare -x
TMPDIR="/var/folders/23/jbv5t1x52bq2rm6yc6xhjtvw0000gp/T/"
declare -x
TOOLBOX="/Applications/MATLAB_R2013a.app/toolbox"
declare -x USER="anna"
declare -x
XAPPLRESDIR="/Applications/MATLAB_R2013a.app/X11/app-defaults"
declare -x
XFILESEARCHPATH="/System/Library/Frameworks/JavaVM.framework/lib/locale/%L/%T/%N%S:"
declare -x
XKEYSYMDB="/Applications/MATLAB_R2013a.app/X11/app-defaults/XKeysymDB"
declare -x __CF_USER_TEXT_ENCODING="0x1F6:0:0"
declare -x com.apple.java.jvmMode="client"
declare -x com.apple.java.jvmTask="JNI"
So, you were right, the fsldir is not part of the PATH and
FSLOUTPUTTYPE isn't set, at least from Matlab's perspective.
Seems like all I have to do is to set them, but that's where
I fail. Matlab doesn't understand setenv and getenv (I guess
because I'm using a bash shell), instead giving me the usual
"command not found". It doesn't protest at echo and export,
but neither does
have an effect - echo FSLOUTPUTTYPE remains empty. Same for
my attempts of using export to edit the PATH variable. It
simply stays the same before and after the command.