Hm, the brainmask is mapped from the base to the individual TP space and then the T1 image of the TP is masked to create the brainmask for the specific TP. That means the brainmask should look exactly like the T1 for all voxel within the mask. (And therefore very similar to the orig, except for intensity scaling). Make sure you are - looking at the same slice and - set the Brightness/Contrast and Min/Max values to agree for both images. Probably the voxels you see are part of the background, but because the brightness is so high, they appear in one image but not in the other.
Martin On Tue, 2010-04-06 at 14:32 -0500, Guang Zeng wrote: > Hello, Martin > > Yes, the longitudinal brainmask I meant is the brainmask.mgz in the > longitudinal dir, not from the base template. > > Thanks! > Guang > > > ______________________________________________________________________ > From: mreu...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > Date: Tue, 6 Apr 2010 12:27:19 -0400 > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Is this longitudinal result correct > > Hi Guang, > > > what do you mean with 'longitudinal brainmask'? > You need to overlay the segmentation to the brainmask in the > longitudinal subject dir. The brainmask in the base dir is in a > different space. > > > Best > Martin > > On Apr 6, 2010, at 11:29, Guang Zeng <freesurfer...@hotmail.com> > wrote: > > > > Hi, there, > > I ran the freesurfer longitudinal stream to analysis scans > from two tps. > I attached the segmentation results of one time-point to its > orig.mgz and the longitudinal brainmask, > I can see part of the brainmask are not labeled, I understood > that it is because of the brainmask is the mean or median of > the norm.mgz from different time points. Just wanna double > check that the results is ok. > > Thanks! > Guang > > > ______________________________________________________________ > The New Busy is not the too busy. Combine all your e-mail > accounts with Hotmail. Get busy. > <11.jpg> > <12.jpg> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ______________________________________________________________________ > Hotmail is redefining busy with tools for the New Busy. Get more from > your inbox. See how. _______________________________________________ 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.
