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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
system('export FSLOUTPUTTYPE="NIFTI_GZ"')
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.

Any idea why?

Thanks!

Anna

On Thu, Jun 13, 2013 at 7:35 PM, Daniel Keeser <[log in to unmask]> wrote:

Hi Anna,

may also try to launch Fsl by typing:
cmd ='/usr/local/fsl/bin/what_ever_you_like_to_start;
system(cmd);

and maybe useful too (advice what the output type should be):
setenv(‘FSLOUTPUTTYPE’, ‘NIFTI_GZ’); (if you like nii.gz or type whatever you like)

Best,
Daniel