Re: [Freesurfer] Is this longitudinal result correct

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

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From: mreuter@nmr.mgh.harvard.edu To: freesurfer_zg@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_zg@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


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