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<font face="Dialog" size="2">Dear Jan-Matthijs,</font> </p>
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<font face="Dialog" size="2">I wasn't aware of this! Thanks a lot dear fieldtrippers, this is surely a helpful addition to ft_volumesegment.</font> </p>
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<font face="Dialog" size="2">Best regards,</font> </p>
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<font face="Dialog" size="2">Gregor</font> </p>
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<font face="Dialog" STYLE="font-size: 10pt"><br>--
<BR>Dr. rer. nat. Gregor Volberg <gregor.volberg@psychologie.uni-regensburg.de> ( mailto:gregor.volberg@psychologie.uni-regensburg.de )
<BR>University of Regensburg
<BR>Institute for Experimental Psychology
<BR>93040 Regensburg, Germany
<BR>Tel: +49 941 943 3862
<BR>Fax: +49 941 943 3233
<BR><a href="http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
">http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
</a><BR><br><br></font>>>> jan-mathijs schoffelen <jan.schoffelen@donders.ru.nl> 5/17/2011 8:42 AM >>><br>Dear Gregor and Younes, </p>
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We recently added functionaity to ft_volumesegment to actually compute the brainmask or scalp surface. Gregor is right in that until a few weeks ago, ft_volumesegment only returned the probabilistic maps for the grey whit and csf compartments. Nowadays, given the appropriate cfg, it can do much more (see the documentation on the wiki for the cfg-settings). For this of course you need an up-to-date version of FieldTrip! </p>
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Best wishes, </p>
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Jan-Mathijs </p>
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On May 17, 2011, at 8:18 AM, Gregor Volberg wrote: </p>
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<font face="Dialog" size="2">Hi Younes,</font> </p>
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<font face="Dialog" size="2">this is actually not a problem with the function. The<span class="Apple-converted-space"> </span></font>"ft_volumesegment"<font face="Dialog" size="2"> will only return segmentations of the anatomical mri with respect to three tissue types: grey matter, white matter, and csf. You can use gray and white matter segmentations to construct your brain compartement by typing e. g. "brain = (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order to get skull and skin compartements, you need your original mri.anatomy which holds the image intensity on a black-to-white scale. You can threshold the white values to segment the head from the background, and this is then your skin compartement (e. g., "skin = (mri.anatomy>300);" as shown in the tutorial). The skull compartement is the oversection of the skin compartement and the brain compartement after you blew up those compartements a bit,</font> </p>
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<font face="Dialog" size="2">skin_a = imerode(skin, s);</font> </p>
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<font face="Dialog" size="2">brain_a = imdilate(brain, s);</font> </p>
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<font face="Dialog" size="2">skull = (brain_a & skin_a);</font> </p>
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<font face="Dialog" size="2">Especially the construction of the skin is a lot of work, as you need the wholes in the anatomical mri (eyes, ear, inhomogeneities) by hand.</font> </p>
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<font face="Dialog" size="2">Best regards and good luck,</font> </p>
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<font face="Dialog" size="2">Gregor</font> </p>
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--<span class="Apple-converted-space"> </span><br style="font-family: Dialog; font-size: 10pt">Dr. rer. nat. Gregor Volberg <<a href="mailto:gregor.volberg@psychologie.uni-regensburg.de">gregor.volberg@psychologie.uni-regensburg.de</a>> (<span class="Apple-converted-space"> </span><a href="mailto:gregor.volberg@psychologie.uni-regensburg.de">mailto:gregor.volberg@psychologie.uni-regensburg.de</a><span class="Apple-converted-space"> </span>)<span class="Apple-converted-space"> </span><br style="font-family: Dialog; font-size: 10pt">University of Regensburg<span class="Apple-converted-space"> </span><br style="font-family: Dialog; font-size: 10pt">Institute for Experimental Psychology<span class="Apple-converted-space"> </span><br style="font-family: Dialog; font-size: 10pt">93040 Regensburg, Germany<span class="Apple-converted-space"> </span><br style="font-family: Dialog; font-size: 10pt">Tel: +49 941 943 3862<span class="Apple-converted-space"> </span><br style="font-family: Dialog; font-size: 10pt">Fax: +49 941 943 3233<span class="Apple-converted-space"> </span><br style="font-family: Dialog; font-size: 10pt"><a href="http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html">http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html<span class="Apple-converted-space"> </span></a><br style="font-family: Dialog; font-size: 10pt"><br style="font-family: Dialog; font-size: 10pt"><br style="font-family: Dialog; font-size: 10pt"></SPAN>>>> Younes Zerouali <<a href="mailto:younes_zerouali@hotmail.com">younes_zerouali@hotmail.com</a>> 5/17/2011 12:25 AM >>><br>Hi all,<br><br>I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (<a href="http://fieldtrip.fcdonders.nl/tutorial/headmodel">http://fieldtrip.fcdonders.nl/tutorial/headmodel</a>).<br>My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before?<br><br>Best,<br><br><br>Younes<br> </p>
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_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a> </p>
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Dr. J.M. (Jan-Mathijs) Schoffelen </p>
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Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands </p>
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<a href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a> </p>
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Telephone: 0031-24-3614793 </p>
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