[FieldTrip] Extracting virtual EEG channel from a patch
Julian Keil
julian.keil at gmail.com
Mon Dec 7 17:57:10 CET 2015
Hi Parinaz,
> My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.
You don't. You compute your virtual channels for a regular grid (something like -20:1:20 for x,y and z) and select the virtual channels in your ROI in a second step.
This might be a bit of an overkill, as you don't use most of your channels later on, but maybe you want to extend your analysis to other cortical areas - you never know.
Anyways, to be more clear: You compute your virtual electrodes on a predefined grid. To find your ROI, you use ft_volumelookup to get a binary matrix which tells you, which voxels of the standard MRI are in your ROI. Then you build a high-resolution grid based on the standard MRI (It's important to use one grid point per voxel). Using pythagoras, you can now find the closest high-resolution grid points for each of your virtual electrodes. As soon as you have these, you can see which of them have a value of 1 in your binary matrix of ft_volumelookup. Now you know which virtual electrodes are inside your ROI.
So for example, you have 2000 virtual electrodes on a -20:1:20 regular grid. You then compute a binary matrix and a high-resolution grid based on the standard MRI resulting in ~900000 grid points on a 91x109x91 grid. Using pythagoras, you find that grid point 6000 is closest to virtual electrode #1. Then you can see if element 6000 from your binary matrix is a 1. If so, your virtual electrode #1 is in your ROI, if not, your virtual electrode is not in your ROI.
> How I can find the atlas position to this maximum point in my code
Do you want to have the coordinates or the actual label? A while ago, I hacked the ft_sourceplot-function to give me the coordinate position as an output, but I can't find the code anymore. I'm sure you can edit the function to also output the label, as this has to be included as a text element somewhere in the function. But please be aware that editing the FT-functions can severely compromise the functionality.
Good luck,
Julian
Am 07.12.2015 um 12:52 schrieb Babaeeghazvini, P.:
> Hi Julian,
>
> Thank you very much for your kind reply. Yes I want to compute virtual channel from an atlas area like whole Precentral_L (not from one voxel in this area). So your second explanation helps me. If I understood correctly in the code below I should use all grid points belong to atlas:
>
> cfg = []
>
> cfg.atlas = atlas;
>
> cfg.roi = atlas.tissuelabel(1)
>
> cfg.inputcoord = 'mni';
>
> mas = ft_volumelookup(cfg,grid);
>
> cfg = [];
> cfg.method = 'lcmv';
> cfg.vol = hdm;
> cfg.grid.xgrid =
>
> cfg.grid.ygrid =
>
> cfg.grid.zgrid =
>
> cfg.grid.inside = 1:size(cfg.grid.pos, 1);
> cfg.grid.outside = [];
> cfg.keepfilter = 'yes';
> source_idx = ft_sourceanalysis(cfg, tlock);
>
> My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.
>
> an other question that I have is that: when I compute the maximum index from
> [maxvalr, maxpowindxr] = max(srcetask.avg.pow)
>
> How I can find the atlas position to this maximum point in my code (I can see this atlas label in the figure that I get from sourceplot, but I want to report this label in matlab)
>
> Regards,
> Parinaz.
>
>
>
>
> From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Julian Keil [julian.keil at gmail.com]
> Sent: Monday, December 07, 2015 9:30 AM
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] Extracting virtual EEG channel from a patch
>
> Hi Parinaz,
>
> I'm not sure if I understood your question correctly.
> Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?
>
> In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.
> In the second case, it's a tad more complicated, but here's how I do it:
> 1. Compute the virtual channels for all grid points in the cortex
> 2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)
> 3. Build a high-resolution 3D-Grid on the standard MRI
> 4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)
> 5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.
>
> I hope this helps, let me know otherwise.
>
> Julian
>
> Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:
>
>> Hello
>>
>> I want to reconstruct a source signal the same as below in page http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors
>> cfg = [];
>> cfg.method = 'lcmv';
>> cfg.vol = hdm;
>> cfg.grid.pos = sourcemodel.pos([maxcohindx maxpowindx], :);
>> cfg.grid.inside = 1:size(cfg.grid.pos, 1);
>> cfg.grid.outside = [];
>> cfg.keepfilter = 'yes';
>> source_idx = ft_sourceanalysis(cfg, tlock);
>> Not from the voxel indicating maximum power ([maxval,
>> maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos
>> = sourcemodel.pos([maxcohindx maxpowindx], :)).
>>
>> Regards,
>> Parinaz.
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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