G'day Bruce et al,
the template is uploading to
ftp://floyd.psy.flinders.edu.au/pub/weber/rh.wholebrain.tif (~5Mb, the
permissions should allow anonymous ftp access). Could you take a look at
it? I guess it's OK but I have no idea what it should look like, maybe it
makes sense in the light of your experience and insight? If you notice any
problems, please let me know. I have been able to view it with
http://www.irfanview.com/
Thanks, Darren
----- Original Message -----
From: "Bruce Fischl" <[EMAIL PROTECTED]>
To: <[EMAIL PROTECTED]>
Sent: Saturday, October 19, 2002 1:18 AM
Subject: Re: mris_make_template etc.
> 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
> >
> >
>
>
