[FieldTrip] error in ft_prepare_headmodel

[Arjen Stolk]

Hi Tom, 

As another work around, you could try using spm12 functionality. cfg.spmversion = ‘spm12’ if the function supports it, or by manually putting it on the path with ft_hastoolbox. There may be differences in the algorithm/outcome between versions, so you may want to be consistent in its use across subjects.

Best,
Arjen

> On Jan 10, 2018, at 12:36 AM, Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl> wrote:
> 
> Dear Tom,
> 
> To me, this looks like a platform/MATLAB version specific issue with the compiled mex-files. Anecdotally, MATLAB2017a on a Mac suffers from not knowing to handle the precompiled stuff that comes with FieldTrip/SPM. Either you could use a lower matlab version (e.g. 2016b, which as far as I know does not suffer from this), or you could try and recompile the affected mex-files from the original c-code with the matlab mex-command. See http://bit.ly/2DeuNlX for more info.
> 
> Best wishes,
> JM
> 
> 
>> On 9 Jan 2018, at 17:27, Tom Marshall <tom.marshall at psy.ox.ac.uk> wrote:
>> 
>> Howdy 'Trippers,
>> 
>> I got a weird error when trying to create a template headmodel using ft_prepare_headmodel (basically just following the steps in the tutorial 'Creating a sourcemodel for source-reconstruction of MEG or EEG data').
>> 
>> After loading and segmenting the template brain I called ft_prepare_headmodel using the suggested parameters.
>> 
>> cfg          = [];
>> cfg.method   = 'singleshell';
>> template_headmodel = ft_prepare_headmodel(cfg, template_seg);
>> 
>> This gave the following error.
>> 
>> Error using ft_notification (line 314)
>> please specificy cfg.tissue and pass an appropriate segmented MRI as input data
>> 
>> Error in ft_error (line 39)
>>   ft_notification(varargin{:});
>> 
>> Error in ft_prepare_headmodel (line 354)
>>           ft_error('please specificy cfg.tissue and pass an appropriate segmented
>>           MRI as input data')
>> 
>> So I added cfg.tissue...
>> 
>> cfg          = [];
>> cfg.method   = 'singleshell';
>> cfg.tissue   = 'brain';
>> template_headmodel = ft_prepare_headmodel(cfg, template_seg);
>> 
>> ...and this upset fieldtrip. After printing 'smoothing brain with a 5-voxel FWHM kernel', it hung for 10-15 minutes, then threw an error with lots of 'Missing symbol' statements (see below - there are a few hundred more, I just copypasted the last two).
>> 
>> Missing symbol '_vm_allocate' required by
>> '/usr/lib/closure/libclosured.dylib->/usr/lib/system/libdyld.dylib->/usr/lib/system/libsystem_platform.dylib->/usr/lib/system/libsystem_pthread.dylib->/usr/lib/system/libcache.dylib->/usr/lib/libgcc_s.1.dylib->/Users/marshall/Documents/MATLAB/fieldtrip-20170726/external/spm8/spm_conv_vol.mexmaci64'
>> Missing symbol '_vm_deallocate' required by
>> '/usr/lib/closure/libclosured.dylib->/usr/lib/system/libdyld.dylib->/usr/lib/system/libsystem_platform.dylib->/usr/lib/system/libsystem_pthread.dylib->/usr/lib/system/libcache.dylib->/usr/lib/libgcc_s.1.dylib->/Users/marshall/Documents/MATLAB/fieldtrip-20170726/external/spm8/spm_conv_vol.mexmaci64'.
>> 
>> Error in spm_smooth>smooth1 (line 105)
>> spm_conv_vol(P,Q,x,y,z,-[i,j,k]);
>> 
>> Error in spm_smooth (line 40)
>>     smooth1(P,Q,s,dtype);
>> 
>> Error in volumesmooth (line 18)
>> spm_smooth(output, output, fwhm);
>> 
>> Error in ft_datatype_segmentation (line 229)
>>           brain = volumesmooth(brain,    smooth,    'brain');
>> 
>> Error in prepare_mesh_segmentation (line 95)
>>     mri = ft_datatype_segmentation(mri, 'segmentationstyle', 'probabilistic',
>>     'hasbrain', 'yes');
>> 
>> Error in ft_prepare_mesh (line 147)
>>     bnd = prepare_mesh_segmentation(cfg, mri);
>> 
>> Error in ft_prepare_headmodel (line 337)
>>         geometry = ft_prepare_mesh(tmpcfg, data);
>> 
>> It seems like the problem is somewhere deep down in spm commands that fieldtrip is calling, so maybe nobody has a clue. I'm hoping somebody has seen this before and knows of a fix...
>> 
>> In case it's relevant: I'm running fieldtrip-20170726 in matlab R2017a on a mac.
>> 
>> And ideas?
>> 
>> Best,
>> Tom
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> 
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