Hi Darren, it looks fairly reasonable, although it's always a bit hard to tell in a non-uniform coordinate system, particularly in color. You can try using mrisp_paint if you want, to paint the frames onto a surface:
mrisp_paint rh.wholebrain.tif#0 $SUBJECTS_DIR/$subject/surf/rh.sphere.reg $SUBJECTS_DIR/$subjects/surf/rh.wholebrain_frame0 would paint the 0th frame, which I think is the average inflated curvature, as a curv file that can be viewed in tksurfer. Frame 3 would then be the average sulc, and frame 6 the average curv (frames 1,4 and 7 are stderrors and 2, 5 and 8 are dofs which won't be very interesting). Bruce On Sat, 19 Oct 2002, Darren Weber wrote: > > 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 > > > > > > > > > > > >
