<div dir="ltr"> Alexander, <div> 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. </div><div> 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". </div><div> </div><div> Wanze</div></div><div class="gmail_extra"><br><div class="gmail_quote">2016-08-05 12:07 GMT-04:00 Nakhnikian, Alexander <span dir="ltr"><<a href="mailto:Alexander_Nakhnikian@hms.harvard.edu" target="_blank">Alexander_Nakhnikian@hms.harvard.edu</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div dir="ltr">
<div style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Hi John,</p>
<p><br>
</p>
<p>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.</p>
<p><br>
</p>
<p>Thanks,</p>
<p><br>
</p>
<p>Alexander</p>
</div>
<hr style="display:inline-block;width:98%">
<div dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> RICHARDS, JOHN <<a href="mailto:RICHARDS@mailbox.sc.edu" target="_blank">RICHARDS@mailbox.sc.edu</a>><br>
<b>Sent:</b> Friday, August 5, 2016 9:51:34 AM<br>
<b>To:</b> <a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>; Nakhnikian, Alexander<br>
<b>Subject:</b> constrain source solution space</font>
<div> </div>
</div>
</div><div><div class="h5">
<font size="2"><span style="font-size:10pt">
<div><a href="https://static-content.springer.com/esm/art%3A10.1007%2Fs10548-016-0505-3/MediaObjects/10548_2016_505_MOESM3_ESM.docx" target="_blank">https://static-content.<wbr>springer.com/esm/art%3A10.<wbr>1007%2Fs10548-016-0505-3/<wbr>MediaObjects/10548_2016_505_<wbr>MOESM3_ESM.docx</a><br>
<br>
1--prepare a grid, for the source volume<br>
2-prepare a head volume<br>
3-prepare electrode (or meg) scalp locations<br>
<br>
These three elements are used for a lead field. <br>
<br>
LF and other elements are used w EEG in ft_sourceanalysis. <br>
<br>
There are several tutorials on FT site to do this. <br>
<br>
John<br>
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Message: 1<br>
Date: Thu, 4 Aug 2016 18:25:38 +0000<br>
From: "Nakhnikian, Alexander" <<a href="mailto:Alexander_Nakhnikian@hms.harvard.edu" target="_blank">Alexander_Nakhnikian@hms.<wbr>harvard.edu</a>><br>
To: "<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>" <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>
Subject: [FieldTrip] Constrain Source solution space<br>
Message-ID:<br>
<<a href="mailto:SN1PR07MB1568036B161E8337E72F69F8B7070@SN1PR07MB1568.namprd07.prod.outlook.com" target="_blank">SN1PR07MB1568036B161E8337E72F<wbr>69F8B7070@SN1PR07MB1568.<wbr>namprd07.prod.outlook.com</a>><br>
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Hello All,<br>
<br>
<br>
I'm trying to constrain my source space to gray matter and I found suggestions for how to do this on the FAQ:
<a href="http://www.fieldtriptoolbox.org/faq/can_i_restrict_the_source_reconstruction_to_the_grey_matter" target="_blank">
http://www.fieldtriptoolbox.<wbr>org/faq/can_i_restrict_the_<wbr>source_reconstruction_to_the_<wbr>grey_matter</a><br>
<br>
[<a href="http://www.fieldtriptoolbox.org/_media/logo-share.png%5D%3Chttp://www.fieldtriptoolbox.org/faq/can_i_restrict_the_source_reconstruction_to_the_grey_matter" target="_blank">http://www.fieldtriptoolbox.<wbr>org/_media/logo-share.png]<<wbr>http://www.fieldtriptoolbox.<wbr>org/faq/can_i_restrict_the_<wbr>source_reconstruction_to_the_<wbr>grey_matter</a>><br>
<br>
faq:can_i_restrict_the_source_<wbr>reconstruction_to_the_grey ...<<a href="http://www.fieldtriptoolbox.org/faq/can_i_restrict_the_source_reconstruction_to_the_grey_matter" target="_blank">http://www.<wbr>fieldtriptoolbox.org/faq/can_<wbr>i_restrict_the_source_<wbr>reconstruction_to_the_grey_<wbr>matter</a>><br>
<a href="http://www.fieldtriptoolbox.org" target="_blank">www.fieldtriptoolbox.org</a><br>
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 ...<br>
<br>
<br>
<br>
<br>
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.<br>
<br>
<br>
Best,<br>
<br>
<br>
Alexander<br>
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