[caret-users] regitering two surface

Donna Dierker donna at brainvis.wustl.edu
Wed Jun 20 09:59:32 CDT 2007


Hi Pedro,

I have zero expericence with EEG, so I don't know what would be best for 
that application.

> I don't need to find a transformation between surfaces having 
> corresponding landmarks, I need to obtain the corresponding landmarks.
But until you register surface A to surface B (or both A and B to C), 
there is no way to establish correspondence between a landmark on 
surface A and the corresponding location on surface B.  Registration 
builds that bridge.

Caret uses landmarks to drive registration, and there is no command line 
method for identifying them yet.  You must draw them for each 
hemisphere.  There are other surface-based registration methods that 
require less/no user input, e.g. FreeSurfer:

http://surfer.nmr.mgh.harvard.edu

It might be possible to jump into the processing stream with already 
generated surfaces, but my hunch is that you'll need to put your T1s 
through the full pipeline.  With 237 scans, I hope you have a lot of CPU 
power.

Donna

On 06/20/2007 09:30 AM, Pedro A. Valdes Hernandez wrote:
> Dear Donna: I'm interested in the surface commonly used for EEG 
> problems. I have 237 T1 MRIs and I'd like to have an automatic command 
> line script to obtain those mean WM-pial surface (if this is the 
> propper surface for my application) and I'd like to have corresponding 
> points between those surfaces. I don't need to find a transformation 
> between surfaces having corresponding landmarks, I need to obtain the 
> corresponding landmarks. Can you help me to understand what software 
> should I download, what should I run and do?
> Any help will be very appreciated
> Thank you in advance
>  
> Pedro
>
>  
> On 6/20/07, *Donna Dierker* <donna at brainvis.wustl.edu 
> <mailto:donna at brainvis.wustl.edu>> wrote:
>
>     Hi Pedro,
>
>     Yes -- Caret does surface-based registration, as described in the
>     registration tutorial:
>
>     http://brainmap.wustl.edu/caret/pdf/Caret_5.5_Tutorial_Segment.pdf
>
>     If these two surfaces are from the same subject, then the core 6
>     landmarks (the set typically recommended for inter-subject
>     registration)
>     will not achieve optimal registration; in that case, additional
>     landmarks (e.g., STS, POS -- as many as you can reliably identify
>     across
>     timepoints) are recommended.
>
>     For each surface, you'll need to use Surface: Geometry: Generate
>     inflated and ellipsoid from fiducial, to generate inputs the above
>     tutorial expects.  You might also consider trying John's new
>     method for
>     registration without flattening:
>
>     http://brainmap.wustl.edu/pub/donna/PUBS/Reg_no_flat_and_new_border_drawing.pdf
>     login pub
>     password download
>
>     I haven't tried it myself yet.  I'm not sure whether your Caret
>     version
>     will include all the features you need to try this.
>
>     Finally, we tend to use the midthickness (fiducial) surface,
>     rather than
>     the WM/GM surface.  We generate a midthickness surface by averaging
>     coordinates of Freesurfer-generated [lr]h.white and [lr]h.pial
>     surfaces.
>
>     Donna
>
>     On 06/19/2007 04:48 PM, Pedro A. Valdes Hernandez wrote:
>     > Hi:
>     > I' completely new in this mailing list so maybe my question is a
>     > little bit foolish
>     >
>     > I have two triangulated WM/GM surfaces, I'd like to know if I
>     can find
>     > corresponding anatomical points between them using CARET/SureFit...
>     >
>     >
>     > Thank you in advance
>     > Pedro
>     >
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