[FieldTrip] constrain source solution space

[Xie Wanze]

 Alexander,
 In John's step 1 (creating the grid, source volume), you exclude the WM
because they WM are fibers not neurons, i.e., they are not generating the
activity.
 In step 2 (creating the head model), you don't exclude the WM. Instead,
you do segmentation of the head/brain, so WM, GM, and OM(CSF) are
separated.  So you are not discarding or losing an "important part of the
volume conductor model".

 Wanze

2016-08-05 12:07 GMT-04:00 Nakhnikian, Alexander <
Alexander_Nakhnikian at hms.harvard.edu>:

> Hi John,
>
>
> Thank you for your feedback. I'm not sure, however, I understand your
> suggestion. Is the idea to exclude the white matter from the head model? If
> so, aren't we discarding an important part of the volume conductor model?
> Furthermore, if I'm correctly interpreting the FAQ page I provided, it
> should be possible to apply a tissue mask after we've completed the 3 steps
> you listed since ft_sourceanalysis and ft_prepare_leadfield are both called
> after we have the grid, head volume, and sensor locations.
>
>
> Thanks,
>
>
> Alexander
> ------------------------------
> *From:* RICHARDS, JOHN <RICHARDS at mailbox.sc.edu>
> *Sent:* Friday, August 5, 2016 9:51:34 AM
> *To:* fieldtrip at science.ru.nl; Nakhnikian, Alexander
> *Subject:* constrain source solution space
>
> https://static-content.springer.com/esm/art%3A10.1007%2Fs10548-016-0505-3/
> MediaObjects/10548_2016_505_MOESM3_ESM.docx
>
> 1--prepare a grid, for the source volume
> 2-prepare a head volume
> 3-prepare electrode (or meg) scalp locations
>
> These three elements are used for a lead field.
>
> LF and other elements are used w EEG in ft_sourceanalysis.
>
> There are several tutorials on FT site to do this.
>
> John
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>    1. Constrain Source solution space (Nakhnikian, Alexander)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Thu, 4 Aug 2016 18:25:38 +0000
> From: "Nakhnikian, Alexander" <Alexander_Nakhnikian at hms.harvard.edu>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Constrain Source solution space
> Message-ID:
>         <SN1PR07MB1568036B161E8337E72F69F8B7070 at SN1PR07MB1568.
> namprd07.prod.outlook.com>
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> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello All,
>
>
> I'm trying to constrain my source space to gray matter and I found
> suggestions for how to do this on the FAQ: http://www.fieldtriptoolbox.
> org/faq/can_i_restrict_the_source_reconstruction_to_the_grey_matter
>
> [http://www.fieldtriptoolbox.org/_media/logo-share.png]<
> http://www.fieldtriptoolbox.org/faq/can_i_restrict_the_
> source_reconstruction_to_the_grey_matter>
>
> faq:can_i_restrict_the_source_reconstruction_to_the_grey ...<http://www.
> fieldtriptoolbox.org/faq/can_i_restrict_the_source_
> reconstruction_to_the_grey_matter>
> www.fieldtriptoolbox.org
> Yes, there are two strategies you can use. You can either make a regular
> 3D grid spanning the whole brain in which only grid locations in grey
> matter are considered ...
>
>
>
>
> The problem is that I cannot figure out how to actually do this. For
> example, I don't see options in ft_sourceanalysis for inputing segmented
> mir with the tissue types of interest, now for giving the program an
> anatomic mask. Any feedback would be greatly appreciated.
>
>
> Best,
>
>
> Alexander
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