Hi Darren,
yes, I think what youu are doing is essentially correct. Don't worry
about the .gcs or tissue_params files, they have nothing to do with the
spherical morphing. The .tif file you create should be a normal multi-frame
tif, with 9 frames in it, made up of 3 sets of 3 (mean,stderror,dof).
These are statistics on the geometric properties of the group of subjects
you gave to mris_make_template in a spherical parameterization (longitude
and lattitude). You should be able to view them in anything that knows how
to read multi-frame tif files I would think.
cheers,
Bruce
p.s. Note that the dof frame has only 1 nonzero element (the 1st), which
should be the # of subjects that make up the template.
--------------------------------------------------------
Bruce Fischl email: [EMAIL PROTECTED]
Mass. General Hosp. NMR Center. tel:(617)-726-4897
Rm. 2328, Building 149, 13th Street fax:(617)-726-7422
Charlestown, MA 02129 USA
On Fri, 18 Oct 2002, Darren Weber wrote:
>
> Dear Bruce et al,
>
> could you please confirm the following is reasonable?
>
> I am trying to register "whole brain" surfaces across subjects, hence
> creating a study specific template (if anyone is interested in the template,
> let me know).
>
> First, run the following to create an individual subject (C01) template:
>
> mris_make_template rh sphere c01
> /usr/local/freesurfer/average/rh.wholebrain.tif
>
> Are any other arguments required? This command, as above, creates the
> output file only, no other files like those in the
> /usr/local/freesurfer/average/ area are created. What are the *.gcs or
> tissue_parms.txt files? The .tif is not a graphics file - what does tif
> stand for? The rh.wholebrain.tif is the same size as other template files,
> so that should be a good sign that it contains the required data.
>
> Then, after spherical transforms for all subjects, the rh.sphere surfaces
> are registered to this individual subject template, using a csh script
> containing:
>
> set avg="/usr/local/freesurfer/average/rh.wholebrain.tif"
> mris_register -curv -w 0 ${sub}/surf/rh.sphere $avg
> ${sub}/surf/rh.sphere.reg
>
> What are the -curv and -w options and how do they affect the registration?
>
> That completes the first pass of the registration process. Then create a
> new wholebrain template, using all subjects' sphere.reg files:
>
> set sub="c01 c02 c03 c04 c05 c06 c07 c08 c09 c10 p02 p04 p05 p06 p07 p08
> p09"
> mris_make_template rh sphere.reg $sub
> /usr/local/freesurfer/average/rh.wholebrain.tif
>
> This should create a template that is the average of all these subjects.
> Then the registration process is repeated to overwrite the sphere.reg files
> for each subject, using the new averaged template.
>
> Is this reasonable? If it has worked correctly, it should now be possible
> to use mris_surfglm on the rh.sphere.reg files.
>
> Thanks, 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
>
>
