Hi Bruce,
It is indeed from the same scan session. I'll wait patiently, let Doug enjoy his vacation before he gets bothered again by all our questions.
Cheers, Ed
On 10 Jul 2012, at 16:57, Bruce Fischl wrote:
Hi Ed,
sorry, you'll have to wait until Doug is back from vacation. Is this from the same session? I've always had it work on flair images using one of the types of initialization.
cheers Bruce
On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
Unfortunately, this has no effect.
Ed
On 10 Jul 2012, at 16:40, Bruce Fischl wrote:
Hi Ed
you are using -t2, right? You can also try -init-header
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
It is slightly better but still displacements in all directions and rotations too exist.
Ed
On 10 Jul 2012, at 16:13, Bruce Fischl wrote:
try -init-spm
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi,
I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap).
The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows:
bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3
and inspected the result with
tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf
The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1.
It makes hardly any difference if instead of --t1 --t2 as contrast setting was used.
Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR?
(FreeSurfer v4.5.0, MacOSX 10.5)
Cheers, Ed _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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