Hi Maryam, it seems very strange that one hemisphere looks ok but other looks bad. In fact, I'd say that it cannot happen. The differences are not likely to be due to version. Can you double check that the tksurfer commands for the lh and rh are the same (except for lh and rh, of course) doug

On 08/22/2012 09:13 PM, Maryam Vaziri Pashkam wrote:

Hi Doug,

I am having a problem with tksurfer overlay function. I ran one analysis in freesurfer 5.1 on a mac machine and I cannot properly load it on the surface. The analysis was performed in the native space. When I use tksurfer to load the analysis on the surface using the overlay function I dont get an error but the output image just shows small dots on the surface instead of patches of activity. It looks like the registration is not correct. I checked the registration on the volume and it looks fine to me. This only happens with one of my subject and only on his left hemisphere. I have attached two tif images called lhnative.tif and rhnative.tif that show the results. I also ran the analysis on the surface for both left and right hemisphere, and it looks fine (lhsurf.tif and rhsurf.tif files attached). Any Idea how to solve this problem? My guess is that the error is in the registration of anatomical volume to anatomical surface in the left hemisphere of this specific subject, but I dont know how to solve this issue.

here is the code that I use to load the data on the surface:

tksurfer teal_tiger_kcb lh inflated -curv -overlay /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz -overlay-reg /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat -scalebarflag 1

Just a note that the recon-all was performed in freesurfer 4.5 and the analysis on freesurfer 5.1. Any chance this might have caused the error?

Thanks, Maryam