[FieldTrip] error in ft_prepare_headmodel

Arjen Stolk a.stolk8 at gmail.com
Thu Jan 11 07:49:44 CET 2018


Glad to see it worked, Tom. Full support for SPM12 has only recently been
completed, with JM laying the last hand on ft_volumenormalization a couple
of weeks ago. Therefore, the issue identified by you might be a missing
link that needs to be created still. Do you think you can you propose your
solution on github, for further joint discussion and implementation?

On Wed, Jan 10, 2018 at 10:42 AM, Tom Marshall <tom.marshall at psy.ox.ac.uk>
wrote:

> Hi Arjen and JM,
>
> Arjen - thanks for the golden tip!
>
> As suggested, I explicitly added the SPM12 toolbox and called it in the
> cfg.
>
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> *[status] = ft_hastoolbox('SPM12', 1, 0); cfg                = [];
> cfg.grid.warpmni   = 'yes'; cfg.grid.template  = template_grid;
> cfg.grid.nonlinear = 'yes'; % use non-linear normalization
> cfg.spmversion     = 'SPM12'; cfg.mri                = mri;
> sourcemodel        = ft_prepare_sourcemodel(cfg); *However, this didn't
> totally solve the problem. At one point in ft_prepare_sourcemodel (line
> 636) ft_volumenormalise is called with a new cfg ('tmpcfg'). The choice to
> use SPM12 doesn't propagate to tmpcfg so fieldtrip adds SPM8 anyway when it
> calls ft_volumenormalise.
>
> I fixed this by adding the following to ft_prepare_sourcemodel at line
> 633...
>
>
> *tmpcfg.spmversion = cfg.spmversion; *
> ...and voila! A nice warped source model :)
>
> Should I file this as a bug?
>
> Best and thanks for the help,
> Tom
>
> ------------------------------
> *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]
> on behalf of Arjen Stolk [a.stolk8 at gmail.com]
> *Sent:* 10 January 2018 16:16
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] error in ft_prepare_headmodel
>
> 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.
>
>
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> *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).
>
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> *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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