I have been following the directions on this site to "deploy" (compile) my MATLAB script so as to be able to run it on launchpad without worrying about MATLAB licenses.

https://nmr.mgh.harvard.edu/martinos/itgroup/deploytool.html

They say that the deployed script cannot do path manipulations such as addpath() or path(path,xxx), so the script should use isdeployed to make sure that such path commands are only executed if isdeployed == 0.

% Only add path if not deployed if isdeployed==0; addpath ~nummenma/matlab/work/connectome/HCP_preproc_tools; end

but then I need to add the path back in again so it can access the functions on that path. In the deploytool GUI I click Settings (the little gear icon), and in the upper window "Additional Parameters passed to MCC:" I inserted

======[ Additional Parameters passed to MCC: ]====== -I ~nummenma/matlab/work/connectome/HCP_preproc_tools mris_gradient_nonlin__unwarp_volume__batchmode_HCPS.m ====================================================

(A web site I found said you need a path to the m-file itself, not just to the directory that contains it, and you separate the path and file)

Then I found I had to circumvent more path(path,xxx) commands in my startup.m file too

======[ startup.m ]====== % If script is not deployed add paths if isdeployed==0; %------------ FreeSurfer -----------------------------% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; %-----------------------------------------------------%

%------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% end =========================

Now at least it compiles without error. But when I run it I get this:

Set up FreeSurfer environment -------- freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 FSFAST_HOME /usr/local/freesurfer/stable5_3_0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /space/ficus/4/users/SNEF_subjects MNI_DIR /usr/local/freesurfer/stable5_3_0/mni FSL_DIR /usr/pubsw/packages/fsl/current ./run_unwarpone.sh /cluster/matlab/8.2 /space/ficus/4/users/SLOTS_sessions_Step/SLOTS010/aahscout/001/001.mgz /space/ficus/4/users/SLOTS_sessions_unwarp/SLOTS010/aahscout/001/001.mgz /space/ficus/4/users/SLOTS_sessions_Step/SLOTS010/unwarpscout001.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cluster/matlab/8.2/runtime/glnxa64:/cluster/matlab/8.2/bin/glnxa64:/cluster/matlab/8.2/sys/os/glnxa64 The file '/usr/local/freesurfer/stable5_3_0/matlab/load_nifti.m' is not in the application's expanded CTF archive at '/homes/6/slehar/.mcrCache8.2/unwarp2'. This is typically caused by calls to ADDPATH in your startup.m or matlabrc.m files. Please see the compiler documentation and use the ISDEPLOYED function to ensure ADDPATH commands are not executed by deployed applications. An error occurred while trying to determine whether "load_nifti" is a function name.

MATLAB:err_while_looking_up_function Error:An error occurred while trying to determine whether "load_nifti" is a function name. Error:Error in mclFreeStackTrace.

Any idea what the problem is now? load_nifti is presumably a FreeSurfer function -- do I now have a problem with my paths to FreeSurfer? I searched my script code and found no explicit call to "load_nifti", I presume that is called deep inside some other function. Should I add the FreeSurfer paths also through the deploytool GUI and not call "nmrenv"?

(from my .cshrc file... alias nmrenv 'source /usr/local/freesurfer/nmr-stable53-env' )