[FieldTrip] compiling ft_volumenormalise

[Anne Urai]

Hi FieldTrippers,

I compile my code to run on the supercomputer cluster (without many matlab
licenses), which usually works fine when I do something like:

*addpath('~/Documents/fieldtrip');*
*ft_defaults; *
*addpath('~/Documents/fieldtrip/external/spm8');*
*mcc('-mv', '-N', '-p', 'stats', '-p', 'images', '-p', 'signal', ...*
*     '-R', '-nodisplay', '-R', '-singleCompThread', fname);*

However, compiling the ft_volumenormalise function gives me some problems.
Specifically, if source is the result of my beamformer analysis, this code

*  cfg                       = [];*
*  cfg.parameter             = 'pow';*
*  cfg.nonlinear             = 'no'; % can warp back to individual*
*  cfg.template               =
'/home/aeurai/Documents/fieldtrip/external/spm8/templates/T1.nii';*
*  cfg.write                 = 'no';*
*  cfg.keepinside             = 'no'; % otherwise, ft_sourcegrandaverage
will bug*
*  source                     = ft_volumenormalise(cfg, source);*

works fine when running it within Matlab. However, when I run the
executable after compiling (which completes without error), a low-level spm
function throws the following error:

*the input is source data with 16777216 brainordinates on a [256 256 256]
grid*
*Warning: could not reshape "freq" to the expected dimensions*
*> In ft_datatype_volume (line 136)*
*In ft_checkdata (line 350)*
*In ft_volumenormalise (line 98)*
*In B6b_sourceContrast_volNormalise (line 57)*
*Converting the coordinate system from ctf to spm*
*Undefined function 'fname' for input arguments of type 'struct'*
*Error in file_array (line 32)*
*Error in spm_create_vol>create_vol (line 77)*
*Error in spm_create_vol (line 16)*
*Error in volumewrite_spm (line 71)*
*Error in ft_write_mri (line 65)*
*Error in align_ctf2spm (line 168)*
*Error in ft_convert_coordsys (line 95)*
*Error in ft_volumenormalise (line 124)*
*Error in B6b_sourceContrast_volNormalise (line 57)*
*MATLAB:UndefinedFunction*

I'd be very grateful for hints from anyone who's successfully compiled the
ft_normalise function! Adding the template T1.nii file, spm8 or freesurfer
at compilation does not solve the problem.
Thanks,

—
Anne E. Urai, MSc
PhD student | Institut für Neurophysiologie und Pathophysiologie
Universitätsklinikum Hamburg-Eppendorf | Martinistrasse 52, 20246 |
Hamburg, Germany
www.anneurai.net / @AnneEUrai <https://twitter.com/AnneEUrai>
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