[FieldTrip] tips for nice sourceplot using 'ortho'

[Eelke Spaak]

Hi Vitoria,

I forgot to add: the default in ft_sourceinterpolate is to *always* use
'nearest' interpolation if the data field is logical (as is the case for
the mask; hence still the blocky masking). This is a reasonable setting I
guess, but I don't see a reason why you shouldn't be able to use 'smudge'
or 'sphere_avg' for a mask as well. You can circumvent this by doing

stat.mask = double(stat.mask);

before the interpolation step.

Best,
Eelke


On 27 February 2014 16:44, Vitoria Piai <v.piai.research at gmail.com> wrote:

>  Hi Elke and Arjen,
>
> Thanks a lot, it almost solved the problem (see figure). It looks better
> than before anyways, so I guess I could just do the finishing in
> Illustrator.
> (Or can you tell from this figure that something is going wrong with the
> interpolation/projection?)
>
> Vitoria
>
>
>
> On 27-2-2014 9:19, Eelke Spaak wrote:
>
> 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?
>
> Best,
> Eelke
>
> On 26 February 2014 22:43, Stolk, A. (Arjen) <a.stolk at fcdonders.ru.nl> <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> <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
>
> _______________________________________________
> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>  --
> 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
> _______________________________________________
> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>  _______________________________________________
> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Vitória Piai
> PhD Candidate
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognition, Radboud University Nijmegen
> Montessorilaan 3, B.02.30
> 6525 HR Nijmegen
> The Netherlands
>
> Email : V.piai at donders.ru.nl
> Phone : +31 24 3612635www.vitoriapiai.com
>
>
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