[FieldTrip] Importing Brainstorm head and source models and leftfields

[Francois Jean Tadel, Mr]

Jeff, Marco:


Good timing, I've been working on similar topics this week. I added processes in Brainstorm to use the forward models in FieldTrip, using ft_volumesegment, ft_prepare_headmodel and ft_prepare_leadfield. For now it is not possible to use the Brainstorm BEM surfaces to compute the leadfield with FieldTrip, but if you think this is useful, we could probably add this.


Before the end of the month, I hope to have all the inverse models available as well. We will have the possibility to call them either with Brainstorm or FieldTrip forward solutions.


I you want to help me with the debugging, or if you want to start working on the inverse/DICS part next week, it's all on github:
https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/process/functions/process_ft_volumesegment.m
https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/process/functions/process_ft_prepare_leadfield.m

You could create a new process to call the FieldTrip function you want, there are already many other examples of wrappers available:
process_ft_channelrepair.m
process_ft_dipolefitting.m
process_ft_scalpcurrentdensity.m
process_ft_timelockstatistics.m
process_ft_sourcestatistics.m
process_ft_freqstatistics.m

If you need help with the plugin API in Brainstorm:
http://neuroimage.usc.edu/brainstorm/Tutorials/TutUserProcess

Functions to convert Brainstorm files into FieldTrip structures:
brainstorm3/toolbox/io/out_fieldtrip_*.m

Cheers,
Francois


________________________________

Hi Marco,

Sorry to say I was not successful, yet. I have shifted to other tasks at this point. I am using 256 channel EEG, and want to use the FreeSurfer cortical ribbon as my source model (I would prefer source/headmodels to be FEM as well). I found that a lot of FieldTrip is based on regular dipole grids, and also it is more oriented to MEG than EEG. I do  not have the time right now to try to put all the pieces together in FieldTrip to do what I want, but might get back to it in a month or two.

Sorry I could not be of more help to you right now.

-Jeff



From: Marco Buiatti [mailto:marco.buiatti at gmail.com]
Sent: Friday, November 04, 2016 3:08 AM
To: FieldTrip discussion list; K Jeffrey Eriksen
Subject: Re: [FieldTrip] importing Brainstorm head and source models and leftfields

Dear all,

I have Jeff's same question. I have anatomies ready in Brainstorm: segmented data imported, co-registration with MEG sensor space, computation of head model with overlapping spheres. Now I would like to import all this into Fieldtrip for source reconstruction of oscillatory sources (DICS).
What's the best way to do this?

And is there any difference between Brainstorm and Fieldtrip in these steps that I should be aware of?

Jeff, did you manage to solve the problem?

Thanks a lot,

Marco

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