<div dir="ltr">Sorry, I meant if you have a 'bnd'. Of course you won't have the 'vol', that is the purpose of calling ft_prepare_headmodel! <div><br></div><div style>Johanna</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">2013/2/6 Johanna Zumer <span dir="ltr"><<a href="mailto:johanna.zumer@gmail.com" target="_blank">johanna.zumer@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Dear Allison,<div><br></div><div>Thank you for your question. There have been some changes to ft_prepare_headmodel recently (partly implemented by me) and my apologies that the documentation for these changes was not made thoroughly. I assume that you are refering to a very recent FT version. :-)</div>
<div><br></div><div>The way that you call ft_prepare_headmodel looks almost correct, except that cfg.vol is not needed. </div><div><br></div><div>If you have already a 'vol' or 'bnd' , then that can be used as the second input argument to ft_prepare_headmodel, and the 'segmentedmri' is not needed.</div>
<div><br></div><div>If you don't already have a 'vol' or 'bnd', then that will be created on the fly within ft_prepare_headmodel from the segmentedmri that you include as second input. However, what are the fields within 'segmentedmri' that you use? If 'brain' or 'scalp' already exist, then those will be found and used by default, and therefore a cfg.tissue is not needed. However, if you have other fields with different names, etc then cfg.tissue should point to the name of the subfield of segmentedmri that you wish to use as the headshape. Please see ft_volumesegment for more details on which tissue types or segmentation types can be computed as output and which can then be used in subsequent functions. Perhaps simply recompute the segmentedmri with the newest version of ft_volumesegment and then it will work?</div>
<div><br></div><div>In the meantime, I will update the documentation to make all this more clear. </div><div><br></div><div>However, one more question. I'm not sure what you mean by the error you get with ft_getopt(cfg,'tissue'). If 'tissue' is not in cfg, then it will return a default empty variable, and there should not be an error. Can you say exactly what line of what function gives the error, and what the error exactly is?</div>
<div><br></div><div>And finally, when you successfully ran singleshell method, was that with the segmentedmri (which would surprise me), or rather with a cfg.headshape option? </div>
<div><br></div><div>Cheers,</div><div>Johanna</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/2/5 Nugent, Allison C. (NIH/NIMH) [E] <span dir="ltr"><<a href="mailto:nugenta@mail.nih.gov" target="_blank">nugenta@mail.nih.gov</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
<div lang="EN-US" link="blue" vlink="purple">
<div>
<p class="MsoNormal">Hello, <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I have what is possibly a naïve question, but I can’t seem to find anything on the tutorial pages.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I’m trying to create a headmodel using the localspheres method, using the output of a segmented MRI.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">There is a tutorial page for using different types of headmodels, but it references ft_prepare_localspheres – which works, but it appears to have been deprecated. When I try this:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">hdr=ft_read_header(‘mydata.ds’);<u></u><u></u></p>
<p class="MsoNormal">cfg=[];<u></u><u></u></p>
<p class="MsoNormal">cfg.method=’localspheres’;<u></u><u></u></p>
<p class="MsoNormal">cfg.grad=hdr.grad;<u></u><u></u></p>
<p class="MsoNormal">cfg.vol=segmented_mri;<u></u><u></u></p>
<p class="MsoNormal">vol=ft_prepare_headmodel(cfg, segmentedmri);<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I get an error at ft_getopt(cfg,’tissue’);<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Although the documentation for ft_prepare_headmodel states that the only additional field needed by localspheres is “cfg.grad” it seems that cfg.tissue may also be required? If so, how do I set this – I can’t find any documentation that
explains.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I should note that I’ve run ft_prepare_headmodel successfully using a singleshell method.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thanks,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Allison<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Allison Nugent, PhD<u></u><u></u></p>
<p class="MsoNormal">MRI Physicist<u></u><u></u></p>
<p class="MsoNormal">Experimental Therapeutics and Pathophysiology Branch<u></u><u></u></p>
<p class="MsoNormal">NIMH/NIH/DHHS<u></u><u></u></p>
<p class="MsoNormal">Ph. <a href="tel:301-451-8863" value="+13014518863" target="_blank">301-451-8863</a><u></u><u></u></p>
<p class="MsoNormal"><a href="mailto:nugenta@mail.nih.gov" target="_blank">nugenta@mail.nih.gov</a><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
</div>
<br></div></div>_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><br>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br></blockquote></div><br></div>
</blockquote></div><br></div>