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
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Keith Duncan