[FieldTrip] tips for nice sourceplot using 'ortho'

[Vitoria Piai]

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> 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
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://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 list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
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> fieldtrip at donders.ru.nl
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-- 
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 3612635
www.vitoriapiai.com

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