[FieldTrip] left to right inversion after source interpolation

[Robert Oostenveld]

Hi Fred,

On http://fieldtrip.fcdonders.nl/faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot there is an explanation to a related question. Also in your case FT_VOLUMERSLICE might be of use. See also http://fieldtrip.fcdonders.nl/faq/what_is_the_plotting_convention_for_anatomical_mris

best
Robert

 

 
On 5 Sep 2012, at 16:30, Kathrin Müsch wrote:

> Dear Fred,
> 
> I encountered a similar thing a while ago and it was because spm8 seems to plot in radiological convention (i.e. left is plotted right and vice versa - http://mailman.science.ru.nl/pipermail/fieldtrip/2012-May/005229.html) so you're plots should actually be correct.
> 
> If you use cfg.interactive = 'yes'; and click into the activated side of the brain, the first coordinate should be negative because you are in the left hemisphere.
> 
> Hope that helps,
> Kathrin
> 
> 
> Am 05.09.2012 um 14:47 schrieb Frederic Roux:
> 
>> Dear fieldtrip users,
>> 
>> I have noticed that after interpolating a dummy source volume with ft_sourceinterpolate,
>> voxels that were located in the left side of the volume, apear to be located in the right
>> side of the volume.
>> 
>> The code that I use is as following:
>> 
>> dummy is a dummy structure of an lcmv beamformer map with the fields
>> 
>> dummy =
>> dim :        [15 18 17]
>> time:        [1x272662 double]
>> pos:         [4590x3 double]
>> inside:     [1x2144 double]
>> outside:   [1x2446 double]
>> method: 'average'
>> avg: [1x1 struct]
>> 
>> voxpos = dummy.pos(dummy.inside,1);% get the coordinates of voxels inside the volume
>> dummy.avg.pow(dummy.inside(sign(voxpos)==1)) = 0; % set activity in the left hemisphere to 0
>> dummy.avg.pow(dummy.inside(sign(voxpos)==-1)) = 1; % set activity in the left hemisphere to 1
>> 
>> cfg = [];
>> cfg.parameters = 'all';
>> 
>> int_dummy = ft_sourceinterpolate(cfg,dummy,template_MNI_mri);
>> 
>> cfg = [];
>> cfg.funparameter = 'avg.pow';
>> cfg.method = 'ortho';
>> 
>> %plot the non-interpolated volume
>> figure;
>> ft_sourceplot(cfg,dummy);
>> 
>> %plot the interpolated volume
>> figure;
>> ft_sourceplot(cfg,int_dummy);
>> 
>> As you can see from the figure in the attachement, the voxels that
>> corresponded to the left hemisphere prior to the interpolation,
>> no appear to be located in the rigth hemisphere.
>> 
>> This is also something that I have observed in real data.
>> 
>> Does anybody have an explanation why this is happening?
>> Am I doing something wrong?
>> 
>> Best,
>> 
>> Fred
>> 
>> 
>> <non_interp_vs_interp.jpg>_______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> --
> Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):
> 
> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg
> 
> Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip