Hi Cedric, when you view it marsbar, are you viewing it on avg152T1.nii? Do avg152T1.nii and DLPFC.nii have the same geometry? To check, look at the qform matrix with: mri_info --vox2ras avg152T1.nii mri_info --vox2ras DLPFC.nii and make sure that they have the same number of rows, cols, slices
doug On 12/12/2012 10:24 AM, Koolschijn, Cédric wrote: > Dear FS-experts, > > I'm trying to follow the instructions on > http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness to > get volumetric stats etc on a functional ROI derived from marsbar. > The tutorial looks all clear to me, however, I have already problems > at the first step. > > If I want to view the ROI I see a big orange square instead of the > specific region. This almost fills the whole brain. > > command: > tkmedit -f avg152T1.nii -overlay DLPFC.nii -fthresh 0.5 > I created the DLPFC.nii in MarsBar (v. 0.42): "ROI definition" > "Export" > > "Export ROI to > image" (select: DLPFC_roi.mat) > from image (select: avg152T1.nii) > save as > DLPFC.nii > > If I view the ROI on marsbar it looks good. Did I miss some prior > step, or is something else wrong? > > Thanks in advance! > > Best wishes, > Cédric > > ------------------------------------------------------------ > P.C.M.P. Koolschijn (Cédric), PhD > Brain and Cognition > Weesperplein 4; Room 3.07 > 1018 XA Amsterdam > The Netherlands > /E /p.c.m.p.koolsch...@uva.nl > /W/ http://home.medewerker.uva.nl/p.c.m.p.koolschijn/ > ------------------------------------------------------------ > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: 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.
