[FieldTrip] [Fieldtrip] creating mni-normalised headmodels of neuromag data

[Hanneke van Dijk]

Hi Jan-Mathijs,

The converting units before ft_prepare_sourcemodel solved it!
I suspected the same, but didn't know at which step it went wrong, and
wasn't aware of the function ft_convert_units...

I will also report it in bugzilla so you have the solution at hand!

Thanks so much!

Hanneke

On Thu, Jun 14, 2012 at 1:13 PM, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Hanneke,
>
> You could try the following:
>
> mri=ft_convert_units(mri, 'mm'), prior to calling ft_prepare_sourcemodel?
> (and then do ft_convert_units(grid,'m') on the output)
>
> Also, what happens if you do cfg.grid.nonlinear = 'no'?
>
> I also saw that you already created a bug on our bugzilla-site. Thanks for
> doing so; we were already aware of your problem and it's on our list to
> look into it in more detail as soon as our time resources allow. At the
> moment I suspect a metric unit issue to be the problem when doing the
> inverse (non-linear) warp.
>
> Best,
>
> Jan-Mathijs
>
>
> On Jun 14, 2012, at 12:47 PM, <Hanneke.vanDijk at med.uni-duesseldorf.de> <
> Hanneke.vanDijk at med.uni-duesseldorf.de> wrote:
>
> Dear all,
>
> I am creating headmodels of neuromag data (Using FT version 20123105 and
> the example script
> http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space)
>
>
> First I realign the mri with the fiducials I get out of mri-lab (in
> voxels).
>
> The 'vol' structure is created like this:
>
> Cfg                            = [];
> cfg.coordsys         = 'neuromag';
> cfg.method           = 'singleshell';
> vol = ft_prepare_singleshell(cfg, segmentedmri);
>
> the 'grid' like this:
>
> load(strcat(basepath,'templates/template_grid.mat'));
> cfg                                = [];
> cfg.grid.warpmni    =  'yes';
> cfg.grid.template   =  template_grid;
> cfg.grid.nonlinear  =  'yes'; % use non-linear normalization
> cfg.coordsys            =  'neuromag';
> cfg.mri                 = mri; %the realigned mri
> grid                     = ft_prepare_sourcemodel(cfg);
>
> Everything works well, untill I plot and see that the sizes/ origins (or
> units) are completely different for the vol and grid. At the moment I
> cannot find a solution. Does anyone have an idea?
> The results are plotted and attached to this e-mail.
>
> Thanks in advance,
>
> Hanneke
>
> p.s. I also filed this in bugzilla, for more information see there:
>
>
> http://bugzilla.fcdonders.nl/buglist.cgi?bug_status=UNCONFIRMED&bug_status=NEW&bug_status=ASSIGNED&bug_status=REOPENED&emailassigned_to1=1&emailreporter1=1&emailtype1=exact&email1=hannekevdg%40hotmail.com&field0-0-0=bug_status&type0-0-0=notequals&value0-0-0=UNCONFIRMED&field0-0-1=reporter&type0-0-1=equals&value0-0-1=hannekevdg%40hotmail.com
>
>
> __________________________________________
>
> Hanneke van Dijk, PhD
>
>
> http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html<
> http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html>
>
>
> Institute for Clinical Neuroscience,
>
> Heinrich Heine Universität Düsseldorf, Germany
>
> Hanneke.vanDijk at med.uni-duesseldorf.de
>
> Tel. +49 (0) 211 81 13074
>
> __________________________________________
>
>
>
>
>
>
>
> <grid_vol.png><grid_vol2.jpg>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> Jan-Mathijs Schoffelen, MD PhD
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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