[FieldTrip] Antw: Segment anatomy from MRI (spm8)

jan-mathijs schoffelen jan.schoffelen at donders.ru.nl
Tue May 17 08:42:22 CEST 2011

Dear Gregor and Younes,

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  

Best wishes,


On May 17, 2011, at 8:18 AM, Gregor Volberg wrote:

> Hi Younes,
> this is actually not a problem with the function. The  
> "ft_volumesegment" 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,
> skin_a  = imerode(skin, s);
> brain_a = imdilate(brain, s);
> skull = (brain_a & skin_a);
> 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.
> Best regards and good luck,
> Gregor
> -- 
> Dr. rer. nat. Gregor Volberg <gregor.volberg at psychologie.uni-regensburg.de 
> > ( mailto:gregor.volberg at psychologie.uni-regensburg.de )
> University of Regensburg
> Institute for Experimental Psychology
> 93040 Regensburg, Germany
> Tel: +49 941 943 3862
> Fax: +49 941 943 3233
> http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
> >>> Younes Zerouali <younes_zerouali at hotmail.com> 5/17/2011 12:25 AM  
> >>>
> Hi all,
> 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 (http://fieldtrip.fcdonders.nl/tutorial/headmodel 
> ).
> 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?
> Best,
> Younes
> _______________________________________________
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> fieldtrip at donders.ru.nl
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Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793

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