Hi,

For one of my subjects, I have noticed a misalignment between sig.nii and orig.mgz when I try to show the sig map using either tkmedit (as below):

cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Analysis
tkmedit-sess -s ../Subjects/auil2 -a OriExp_TR3_1p5mm_PR -c ANG_90_45

or tkmedit-sess:

cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Subjects
tkmedit auil_anat orig.mgz -overlay auil2/bold/OriExp_TR3_1p5mm_PR/ANG_90_45/abs_sig.nii.gz -reg auil2/bold/register.dof6.dat~

I checked the registration file for this subjects and I don't see this problem there.

tkregister2 --reg ../Subjects/auil2/bold/register.dof6.dat~ --mov ../Subjects/auil2/bold/template.nii.gz --surf

I also checked the brain.mask and it covers the whole brain and looks fine to me. I also checked my other subjects and their results are fine.

Do you have any idea why this is happening?

P.S.: I process my data in in nmr-dev-env but I have also checked the above lines in nmr-stable53-env and problem is still there.

Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School