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

Younes Zerouali younes_zerouali at hotmail.com
Tue May 17 16:11:36 CEST 2011

Dear Gregor and Jan-Mathijs,

Thank you both for prompt answers, I'll get to work and try that!



From: jan.schoffelen at donders.ru.nl
To: fieldtrip at donders.ru.nl
Date: Tue, 17 May 2011 08:42:22 +0200
Subject: Re: [FieldTrip] Antw:  Segment anatomy from MRI (spm8)

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 FieldTrip!
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 

>>> 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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fieldtrip at donders.ru.nl
 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The NetherlandsJ.Schoffelen at donders.ru.nlTelephone: 0031-24-3614793 

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