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.Koolschijn@uva.nl /W/ http://home.medewerker.uva.nl/p.c.m.p.koolschijn/
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