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

[jan-mathijs schoffelen]

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120614/b45c662e/attachment-0002.html>