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Hi - you may be able to map the FreeSurfer surface atlases into 3D using their tools, though you might find it easier to use the 3D tools supplied with FSL - see the documentation for details of those. Cheers. On 2 Dec 2008, at 14:08, Hans Odd wrote: > Steve, > > thanks for replying - I'm not sure if you're familiar with > Freesurfer, but they include a cortical brain atlas that divides the > cortical surface into specific areas such as right anterior > cingulate cortex etc. > > My specific need is to coregister this atlas with my T2 data, so > that I can follow white matter tracts and plot termination points to > the cortical surface > > Hans > > > --- On Tue, 12/2/08, Steve Smith <[log in to unmask]> wrote: > >> From: Steve Smith <[log in to unmask]> >> Subject: Re: [FSL] brain atlases >> To: [log in to unmask] >> Date: Tuesday, December 2, 2008, 12:50 PM >> Hi - its not clear exactly what kind of atlas you are asking >> about? >> Cheers. >> >> >> On 2 Dec 2008, at 09:16, Hans Odd wrote: >> >>> Dear FSL team, >>> >>> I was recommended to use FSL by the team supporting >> Freesurfer, because my research data is T2 weighted >> MRI's >>> >>> I've download FSL and am beginning to tinker with >> it - there are a few questions that don't appear to be >> answered on the FAQ page. >>> >>> My research project concerns white matter tracks and >> ageing. I wish to match WMT's to the cortical surface >> anatomy - does FSL include such atlases in its package or >> can I import an atlas? >>> >>> Many thanks for any help you can shed on this matter, >>> >>> Hans Odd >>> >> >> >> --------------------------------------------------------------------------- >> Stephen M. Smith, Professor of Biomedical Engineering >> Associate Director, Oxford University FMRIB Centre >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 222726 (fax 222717) >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >> --------------------------------------------------------------------------- > > > > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------