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, sha...@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 >> 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/ >> >> >> > -- 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.
