On 16 Jul 2012, at 18:00, freesurfer-request@nmr.mgh.harvard.edu wrote:

Message: 18

Date: Mon, 16 Jul 2012 11:32:06 -0400

From: Douglas N Greve <greve@nmr.mgh.harvard.edu>

Subject: Re: [Freesurfer] How to register FLAIR to T1?

To: freesurfer@nmr.mgh.harvard.edu

Message-ID: <500433F6.8010102@nmr.mgh.harvard.edu>

Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Often with FLAIR there is not enough gray-white contrast to run the

registration. Try using the pial surface instead, with "-surf pial --t1"

This tells it to use the pial surface as a boundary. The --t1 is needed

because the intensity should go from bright to dark. Let me know if that

does not fix the problem.

doug

On 07/10/2012 11:58 AM, Bruce Fischl wrote:

glad to hear it :). You may need to repost (and possibly upload your

data)

On Tue, 10 Jul 2012, Ed Gronenschild wrote:

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

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--

Douglas N. Greve, Ph.D.

MGH-NMR Center

greve@nmr.mgh.harvard.edu

Phone Number: 617-724-2358

Fax: 617-726-7422