Hi Darren, that's pretty much the way I generated the lh and rh templates we use. There's a binary named mris_make_template,which you probably have, that will take a bunch of surface models and construct a template (.tif) from them. You'll have to name the individual surface lh or rh, since it's expecting a hemisphere. The mris_register binary is actually smart enough to change it's default parameters if the target is from a single surface (it uses a more rigid morph).
Good luck, Bruce On Fri, 11 Oct 2002, Darren Weber wrote: > > Dear Bruce et al, > > my query is about how to register cortical surfaces across X subjects, given > that we have modified the usual left/right surface separation. > > Some time ago we discussed how to extract a complete cortical surface, > rather than the left/right hemi surfaces. The purpose of this being to use > a complete cortical surface for ERP/MEG source modelling methods. This > involves a couple of modifications to the wm volume and the usual inputs to > the fill white matter process (see attached shell script for details). In > my case, the resulting surfaces are called rh.*, although they actually > contain both left and right hemispheres, joined by the corpus callosum (not > strictly cortex, but unavoidable in this approach). For source modelling, > these surfaces are nice. > > Having obtained these surfaces for nearly 20 subjects, we've raised the > possibility of doing a cortical thickness analysis for two groups, controls > and PTSD patients. This requires that any vertex A is located in the same > coordinate system and location for all subjects, so they must be > coregistered (Fischl et al, 1999, Human Brain Mapping 8:272-284; > http://www3.interscience.wiley.com/cgi-bin/issuetoc?ID=67501785). > > Normally, I assume the registration process morphs each left/right hemi > cortex into two unit spheres (rather than morphing each hemi cortex onto the > left/right hemisphere of one unit sphere). So, many of the examples in > Fischl et al (1999) illustrate one hemisphere or another. Thus, we normally > have lh.sphere and rh.sphere, two unit spheres, one for each hemi cortex > surface. Further, the spherical sulcal patterns of each lh.sphere and > rh.sphere are then further morphed (non-linear) to match the patterns of > some average template. Obviously the whole cortical surfaces we have are > not separated into lh/rh, rather the rh contains both. > > My concern here is with this template - I don't know much about it. I > assume the template (average7) is specific for each left/right hemi-cortex. > It might not be a good template for our data, which contains the whole > cortex, including the "sagittal fissure" and corpus callosum. > > Can you recommend a template for registration of these subjects' surfaces? > Is it reasonable to use one subject surface as a template for all others? > If so, what do you think of a two stage process, first registering all > subjects to subject X, then averaging across all subjects to create a study > specific average, then reregister all subjects to this average? > > Many thanks for your consideration, Darren > > > -- > Darren Weber, PhD Student > Cognitive Neuroscience, School of Psychology > Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust. > Ph: (61 8) 8201 3889, Fax: (61 8) 8201 3877 > http://203.3.164.46/~dlw/homepages/index.html >
