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my suggestion gives you the centre of gravity of an ROI, and Dave's gives you the coordinate of the mode of the atlas probability map. So Dave's approach is probably more accurate for your purposes. Saad. On 31 Jul 2009, at 19:50, Iwo Bohr wrote: > However Saad's approach seems to produce slightly different results, > seemingly more accurate (I am in process of comparing these two), I > wonder what it is due to? Not that it would matter for my purposes, > but just out of curiosity. > Iwo > > Date: Fri, 31 Jul 2009 14:43:10 +0100 > From: [log in to unmask] > Subject: Re: [FSL] coordinates extraction from atlas > To: [log in to unmask] > > Oh that's even better! > > > On 31 Jul 2009, at 14:03, David Flitney wrote: > > Take a look at the atlas definition files in /usr/local/fsl/data/ > atlases. The xml files have a maximum probability location for each > atlas object - so that fslview can jump to object when selected in > the GUI. > > Hope that helps. > > Dave > > On 31 Jul 2009, at 13:54, Iwo Bohr wrote: > > Hello FSL experts, > > I would like to draw a plot with rois from Harvard-Oxford atlas > represented as points in it (nodes of functional network). For this > purpose I need to extract approxiamte coordinates of atlas rois (to > be used in gplot function in Matlab), it does not have to be very > precise location, eg it may be a point corresponding somehow to a > "centre" of a roi, however it may be defined. > I thought that atlasquery may offert a facility like this, but it > doesn't appear to be the case (at least I couldn't find an option > like this). > I am happy to hear any suggestions how to approach this problem. > Many thanks in advance, > Iwo > > Share your memories online with anyone you want. Learn more. > > -- > Dave Flitney, IT Manager > Oxford Centre for Functional MRI of the Brain > E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717 > URL: http://www.fmrib.ox.ac.uk/~flitney > > > > > -- > Saad Jbabdi > University of Oxford, FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > +44 (0) 1865 222523 (fax 717) > www.fmrib.ox.ac.uk/~saad > > > > > > > > > > Celebrate a decade of Messenger with free winks, emoticons, display > pics, and more. Get Them Now -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK +44 (0) 1865 222523 (fax 717) www.fmrib.ox.ac.uk/~saad