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 gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
