Hi Shahin, I finally tracked it down. The problem is that in the analysis you specified -native but after that you specified -per-run. These two are incompatible, so it uses whatever is specified last. This caused it to take the intersection of all the run masks. But the run masks are not registered to each other, so the intersection became much smaller than the original masks. Reanalyze without -per-run and see if that helps things. I've put an error trap in the new version of mkanalysis-sess to prevent this in the future. doug

On 11/14/2014 03:05 PM, shahin@nmr.mgh.harvard.edu wrote:

Hi Doug,

It is: /cluster/tootell/pitcairn/1/users/good_subjects_anat

...

what is your SUBJECTS_DIR ? On 11/14/2014 11:22 AM, SHAHIN NASR wrote:

...

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/