[FieldTrip] General questions

["Jörn M. Horschig"]

Dear Vahe,

thanks for your elaborate feedback. Of course, we are working hard to 
make FieldTrip more intuitive and user-friendly. We are quite aware that 
there are lot of things which are suboptimal, some of them that you also 
pointed out. Here's my comments on your points:


> 1. I understand that fieldtrip is a data analysis toolbox, however the
> results of the analysis need to be visualized. I find the fieldtrip
> visualization functions, especially of the source analysis results (e.g.
> ft_sourceplot, ft_sourceinterpolate, ft_sourcemovie) inadequate.
> My question is how do you usually visualize the results of the source
> analysis? Do you write your own matlab functions, including font-ends to
> fieldtrip plotting functions or you use other freely/commercially available
> tools that can import fieldtrip structures or you are satisfied with what is
> provided in the fieldtrip toolbox?

What exactly do you find inadequate? The way the plots look like or the 
way you need to call the functions? I have to admit that plotting 
results in sourcespace is more complex than plotting in sensor space. 
This is simply because there are so many more options and parameters. 
The intention of FT is not to provide the user with an easy-to-click GUI 
which hides important options, but to require the user to think 
him-/herself about important options like downsampling, interpolation 
options, normalization, etc. (to answer your question on my behalf: I am 
satisfied, once I found out how to plot - which took some time).

> 2. It seems that the documentation provided on the fieldtrip website is not
> very up-to-date and the descriptions of many configuration options in the
> *.m files are not documented. At the moment to understand all the available
> configuration options, and what different functions are doing and how they
> are implemented, I am debugging them step-by-step.
> Short of debugging or every time asking questions in this list, is there
> another way of getting information about all the available configuration
> options for different fieldtrip functions and their implementation details?
Yes, there is an overview other than what the help is showing:
http://fieldtrip.fcdonders.nl/reference/index
For a function overview:
http://fieldtrip.fcdonders.nl/reference

The function and configuration reference of the FieldTrip wiki is 
literally a collection of all the helps. Note that for some functions, 
there are undocumented functions (which has a reason), they are mostly 
hidden and explained in the comments below the help.  We (will) try to 
make the naming consistent throughout FieldTrip, so that, once 
acquainted with the naming scheme, the cfg options should be 
self-explanatory. Can you point to a particular example where the 
cfg-options are not documented adequately? This is for us sometimes a 
bit hard to figure out, because we know FT already quite well and thus 
need to rely on feedback of new users. But if you have any questions how 
a certain function works, or about the algorithm behind, feel free to 
just write a mail to this list - that's what it is there for ;)

> 3. I found some functions in the fieldtrip's SVN (trunc) version (on
> googlecode), which are not available in the daily releases on the ftp server
> (e.g. ft_surfacecheck).
> Is it safe to use those functions (I understand that the toolbox is released
> under GPL)?
Sorry, I don't know as I have neither written nor used these functions.

> 4. Are the measurement units used throughout fieldtrip functions basic SI
> (International System of Units) units? More specifically, what are the units
> of the inputs to ft_dipolesimulation (cfg.dip.signal, cfg.dip.amplitude)?
> Are they A*m or nA*m or something else? What are the units of the output
> from the minimumnormestimate? A/m?

I also cannot be of much help here, but as far as I know unit 
declaration are a consistent problem throughout FieldTrip, and currently 
we are working on restructuring the code and making this clearer.  I 
would be tempted to say that the unit is a 'what-you-put-in-comes-out', 
i.e. if your data is measured in nA and the distance measured in cm, 
then the unit will be nA*cm. But, I don't know exactly. You can try to 
search the FieldTrip wiki for 'units' or any related search term, but I 
am afraid that most pages will be rather a collection of To-Dos for/from 
one of us.
Maybe mire helpful might be this to search in the mailinglist for old 
posts on units (I couldn't find any, sorry)"
http://fieldtrip.fcdonders.nl/discussion_list

I hope Robert or Jan-Mathijs (currently on vacation) can give you more 
elaborate feedback on the last two question of yours.

Best,
Jörn

>
>
> Thanks in advance
>
> Vahe Poghosyan, Ph.D.
> Senior Scientist
> Lab. for Human Brain Dynamics
> AAI Scientific Cultural Services Ltd.
> http://aaiscs.com/LHBD/
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group

P.O. Box 9101
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