First thing you can do is to look at each individual in the ces file,
tksurfer fsaverage lh inflated -ov eccen/ces.000.nii.gz
Bring up the functional configuration window. You may need to adjust the
thresholds. Then scroll through each time point. The pattern itself
might not be meaningful, but y
Michelle Umali wrote:
> Hi Doug,
> Thank you for your help with this. So when I looked at the maps, two
> issues arose.
>
> 1) The fieldsign map looks like it needs lots of smoothing. When I
> ran the individual subjects on the surface, I smoothed by 20 during
> fieldsign-sess. Is it still
Hi Doug,
Thank you for your help with this. So when I looked at the maps, two issues
arose.
1) The fieldsign map looks like it needs lots of smoothing. When I ran the
individual subjects on the surface, I smoothed by 20 during fieldsign-sess.
Is it still appropriate/can one smooth at the mri_fie
Hi Michelle, try this:
isxconcat-sess -sf sessidlist -a rtopy.fsaverage.lh -call -o retgroup
cd retgroup/rtopy.fsaverage.lh
mri_glmfit --y eccen/ces.000.nii.gz --osgm --o eccen/glm.real --surface
fsaverage lh
mri_glmfit --y eccen/ces.001.nii.gz --osgm --o eccen/glm.imag --surface
fsaverage lh
m
Hi Doug and the Freesurfers,
Thanks for your help. I have 2 questions.:
1) I did the retinotopy analysis on the fsaverage surface as you suggested
below and then ran isxconcat-sess for my eccen and polar data:
e.g. isxconcat-sess -analysis rtopy.fsaverage.lh -contrast polar -sf
sessid -o group
Hi Doug,
I'm a little confused as to how to assign functional data to the fsaverage
space.
1) Do you mean just change each subject's subjectname file to fsaverage and
then do the same thing as before for each person?
2) Also, when I specify the analysis do I change -rtopy.self.lh to
rtopy.fsaverag
If you want to combine across subjects, then you need to run the
analysis on fsaverage (ie, rerun preproc-sess, create a new analysis,
run selxavg3-sess, and then isxconcat-sess).
doug
Michelle Umali wrote:
> Dear Freesurfers,
> I've generated individual polar, eccentricity, and fieldsign maps f
Dear Freesurfers,
I've generated individual polar, eccentricity, and fieldsign maps for each
of my subjects. I would like to generate group average maps of these that I
can visualize on the fsaverage brain.
When I ran:
isxconcat-sess -sf sessid -analysis rtopy.self.lh -o group_lh
I got:
ERROR: an
