[FieldTrip] tips for nice sourceplot using 'ortho'

Eelke Spaak eelke.spaak at donders.ru.nl
Thu Feb 27 09:19:55 CET 2014

Hi Vitória,

When you are calling ft_sourceinterpolate, you can call it with
different interpolation methods. I think the default is 'nearest',
which results in interpolated blocky figures. You can also specify
cfg.interpmethod = 'sphere_avg' or cfg.interpmethod = 'smudge', both
of which result in smoother interpolations.

Furthermore you can play around with the mask variable for plotting. I
guess you are now using the binary mask resulting from the output of
ft_sourcestatistics. You can also create a real-value mask based e.g.
on the statistical or relative values (which results in opacity being
ramped up according to effect size), and then apply the statistical
map to that. This would be something like the following:

tmp = int_stat.stat;
oldmask = int_stat.mask;
int_stat.mask = (tmp - min(tmp(:))) ./ (max(tmp(:)) - min(tmp(:))); %
set the new mask to range between 0 and 1
int_stat.mask(oldmask < 0.9) = 0; % mask out non-significant voxels

where int_stat is the result of ft_sourceinterpolate. Note that
because I used 'sphere_avg' interpolation in this case, the
interpolated mask will not be strictly binary anymore, hence the test
< 0.9, rather than == 1. (Also note that you should specify
cfg.opacitylim = [0 1] and cfg.opacitymap = 'rampup' when plotting
with a mask like the above.)

Does this do something like you want?


On 26 February 2014 22:43, Stolk, A. (Arjen) <a.stolk at fcdonders.ru.nl> wrote:
> Hi Vitoria,
> I don't know whether you have done so already, but you could try and interpolate your source reconstructed activity on a high spatial resolution version of a brain (e.g. try the /template/anatomy/single_subj_T1_1mm.nii). Hope this helps,
> Arjen
> ----- Oorspronkelijk bericht -----
>> Van: "Vitoria Piai" <v.piai.research at gmail.com>
>> Aan: fieldtrip at donders.ru.nl
>> Verzonden: Woensdag 26 februari 2014 19:03:55
>> Onderwerp: [FieldTrip] tips for nice sourceplot using 'ortho'
>> Hi all,
>> Does anyone have some tips for getting a nice sourceplot using the
>> 'ortho' method?
>> I'm using functional data masked by the stats results. I see a lot of
>> cerebellum activity as well as deeper sources, so a surface plot is
>> very
>> likely to be fooling me. I'm getting a very ugly figure, though,
>> because
>> of all the squares (activity and masks) bleeding outside of the skull
>> outline.
>> Anyone with experience on what works well to make that look nicer
>> (eg.,
>> in Illustrator)?
>> Thanks, Vitoria
>> _______________________________________________
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>> fieldtrip at donders.ru.nl
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> --
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Email:  a.stolk at donders.ru.nl
> Phone:  +31(0)243 68294
> Web:    www.arjenstolk.nl
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