[FieldTrip] odd interaction between matlab and ft version in ft_volumerealign

Fri May 6 10:22:58 CEST 2016

Hi,

thanks, I will look into it!

One of the problems below we have been consistently experiencing here is 
related to the headshape structure: to avoid errors, we have been doing:

hs.pnt=hs.pos;

Cheers,

	Bruno

On 05/05/2016 20:05, Schoffelen, J.M. (Jan Mathijs) wrote:
> Hi Bruno,
>
> I think we have just been looking into it. And with just, I mean really
> just. I just merged a pull request from Roemer van der Meij into
> github.com/fieldtrip/fieldtrip
> <http://github.com/fieldtrip/fieldtrip> (#141). This merge is related to
> a graphics issue that needs to be resolved differently for different
> matlab versions (in particular for matlab>=2014 it requires a different
> solution than matlab<2014). I wonder whether this is related to the
> problem you report.
> We did not do an comparable extensive sweep of the possible combinations
> (i.e. matlab versions and fieldtrip versions), so could you pull a copy
> from git and try it out? We have a ‘tutorial’ on the fieldtrip wiki that
> explains one way of getting yourself a local copy of the code.
>
> Thanks,
>
> Jan-Mathijs
>
>
>
>
>
>> On 05 May 2016, at 20:37, Bruno L. Giordano <brungio at gmail.com
>> <mailto:brungio at gmail.com>> wrote:
>>
>> Hello,
>>
>> I am trying to run these commands on different matlab versions(2013
>> vs. 2015) and using different FT versions (20141209 vs. 20160317;
>> let's call them 2014 vs. 2016).
>>
>> The code I run is as follows:
>>
>> mri=ft_read_mri(mrifilename,'dataformat','nifti_spm');
>>
>> cfg=[];
>> cfg.method='fiducial';
>> cfg.coordsys='4d';
>> cfg.fiducial.nas=[59 168 104];
>> cfg.fiducial.lpa=[138 133 28];
>> cfg.fiducial.rpa=[147 138 169];
>> mri=ft_volumerealign(cfg,mri);
>>
>> hs=ft_read_headshape(headshapefilename);
>> % hs.pnt=hs.pos; %required for later fieldtrip versions or gives an
>> error, see v
>>
>> cfg=[];
>> cfg.method='headshape';
>> cfg.headshape=hs;
>>
>> mrihs=ft_volumerealign(cfg,mri);
>>
>> Unless otherwise noted, the code fails when I quit the interactive
>> alignment window.
>>
>> It fails in the following cases (errors below):
>> Matlab: 2015; FT: 2016
>> Matlab: 2015; FT: 2014
>> Matlab: 2013; FT: 2016
>>
>> and is successful only for
>> Matlab: 2013; FT: 2014
>>
>> Did anyone experience similar problems? Is there a workaround? If not,
>> would it be complicated to estimate the transformation matrices myself
>> once I know the right scale/translation/rotation parameters?
>>
>> Thank you,
>>
>> Bruno
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Matlab: 2013; FT: 2016
>> Matlab: 2013; FT: 2016
>> Fails when quitting interactive alignment window
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>> Error using cell/ismember>cellismemberR2012a (line 193)
>> Input A of class cell and input B of class cell must be cell arrays of
>> strings, unless one is a string.
>>
>> Error in cell/ismember (line 57)
>>    [varargout{1:max(1,nargout)}] = cellismemberR2012a(A,B);
>>
>> Error in ft_senstype (line 303)
>>    if     (mean(ismember(ft_senslabel('ant128'),         sens.label))
>> > 0.8)
>>
>> Error in ft_datatype_sens (line 138)
>> ismeg = ft_senstype(sens, 'meg');
>>
>> Error in ft_checkconfig (line 250)
>>  cfg.elec = ft_datatype_sens(cfg.elec);
>>
>> Error in ft_interactiverealign (line 71)
>> cfg.template   = ft_checkconfig(cfg.template, 'renamed', {'vol',
>> 'headmodel'});
>>
>> Error in ft_volumerealign (line 691)
>>      tmpcfg = ft_interactiverealign(tmpcfg);
>>
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Matlab: 2015; FT: 2016
>> Matlab: 2015; FT: 2016
>> hs.pnt=hs.pos; %required or will give another error
>> Fails when quitting interactive alignment window
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>> Error using  *
>> Inner matrix dimensions must agree.
>>
>> Error in ft_sourceinterpolate (line 328)
>>        av     = interpmat*fv;
>>
>> Error in ft_volumerealign (line 752)
>>      smoothdist          = ft_sourceinterpolate(tmpcfg, functional,
>> target);
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Matlab: 2015; FT: 2014
>> Matlab: 2015; FT: 2014
>> hs.pnt=hs.pos; %required or will give another error
>> Fails when creating the interactive alignment window
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>>
>> ield assignment to a non-structure array object.
>>
>> Error in ft_plot_mesh (line 61)
>>  bnd.pnt = bnd;
>>
>> Error in ft_interactiverealign>cb_redraw (line 282)
>>    ft_plot_mesh(template.elec.chanpos,'vertexcolor', 'b',
>> 'vertexsize',10);
>>
>> Error in ft_interactiverealign (line 126)
>> cb_redraw(gca);
>>
>> Error in ft_volumerealign (line 584)
>>      tmpcfg = ft_interactiverealign(tmpcfg);
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Bruno L. Giordano, PhD
>> Institute of Neuroscience and Psychology
>> 58 Hillhead Street, University of Glasgow
>> Glasgow, G12 8QB, Scotland
>> T +44 (0) 141 330 5484
>> Www: http://www.brunolgiordano.net <http://www.brunolgiordano.net/>
>> Email charter: http://www.emailcharter.org/
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>
>
>
>
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Bruno L. Giordano, PhD
Institute of Neuroscience and Psychology
58 Hillhead Street, University of Glasgow
Glasgow, G12 8QB, Scotland
T +44 (0) 141 330 5484
Www: http://www.brunolgiordano.net
Email charter: http://www.emailcharter.org/