Thanks, Bruce.
mris_make_template --help stops at 'valid options are:' :-( One of the input parameters is a surface name - I suppose 'orig', 'white', 'pial' etc are valid. I'm not sure what surface to specify; is it 'sphere' or 'inflated' or something else? Cheers, Darren ----- Original Message ----- From: "Bruce Fischl" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Friday, October 11, 2002 12:12 PM Subject: Re: registration of whole cortical sheet > 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 > > > >
