No problem. What I would do is create a surface-based label file with the
peak in each subject, then use mris_spherical_average to generate an
average label (this will be in spherical coords). A typical command line
would be:
set average_subject=fsaverage
mris_spherical_average -osurf sphere -sdir $SUBJECTS_DIR -n -o
${average_subject} label ${hemi}.$label $hemi sphere.reg $SUBJECTS \
$SUBJECTS_DIR/${average_subject}/label/${hemi}.$label.label
note that the -n means "normalize" so that it will divide by the total
number of subjects. Taking this out will make the output in [0 nsubjects]
instead of [0 1]. You can then load the the average label in tksurfer on
the fsaverage subjects, use tools->label->copy label statistics to overlay,
and directly visualize the probability of each point on the surface being
in the label.
cheers,
Bruce
On Fri, 12 Sep 2008, Keith
Duncan wrote:
Hi Bruce,
Basically I have data from 45 subjects, and I would like to show the
variability in the location of the individuals peak activation. They are all
on the ventral surface, and are in occipitotemporal sulcus and fusiform gyrus
- so ideally I'd like to use the inflated brain as it would nicely illustrate
the variability The peaks could be represented by crosses or dots, but they'd
have to be small enough, too big and the 45 peaks would end up looking like
an activation map. Would this be possible using the annotation file? If so,
how do I go about writing one? (Sorry if this is a basic question - I've just
started using Freesurfer....)
Thanks again,
Keith
Bruce Fischl wrote:
Hi Keith,
I guess you could write your cross locations into an annotation file then
they would be displayed as small colored patches. I'm not sure which figure
you are referring to, or exactly what you're trying to do though.
Bruce
On Fri, 12 Sep 2008, Keith Duncan wrote:
I've just read Fisch et al 2007 (Cerebral Cortex) where Figure 1 (I think
made in tkmedit) shows canonical slices with small green crosses - is
there a way to do a similar thing (preferably not by placing the crosses
manually) on the inflated brain?
Thanks again,
Keith
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