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

Gregor Volberg Gregor.Volberg at psychologie.uni-regensburg.de
Tue May 17 08:18:39 CEST 2011

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, 

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

>>> 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?



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