[MINC-users] How to register T1 onto T2/PD?

[Ed Gronenschild]

Thank you for your response.
The problem was solved by adding -nothreshold option

without -nothreshold I got the following transformation matrix:
-center         0.00000    0.00000    0.00000
-translation   -0.42123    0.01528   -1.36785
-rotation      -0.13077    1.24821    1.40240
-scale          1.00000    1.00000    1.00000
-shear          0.00000   -0.00000    0.00000

and with -nothreshold -close:
-center         0.00000    0.00000    0.00000
-translation   -0.08993    1.40369  -37.71188
-rotation       2.91978    5.85738    2.30537
-scale          1.00000    1.00000    1.00000
-shear         -0.00000   -0.00000    0.00000

and with -nothreshold -far:
-center         0.00000    0.00000    0.00000
-translation    0.05671    1.00988  -38.10320
-rotation       1.98986    5.50084    2.33306
-scale          1.00000    1.00000    1.00000
-shear         -0.00000   -0.00000   -0.00000

There is only a marginal difference between -close [default] and -far
options in this case. Note the effect on the Z translation by adding
-nothreshold option.

Ed

On 17 Oct 2008, at 18:00, minc-users-request at bic.mni.mcgill.ca wrote:

> Message: 4
> Date: Fri, 17 Oct 2008 11:13:56 -0400 (EDT)
> From: Claude LEPAGE <claude at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] How to register T1 onto T2/PD?
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID: <200810171513.m9HFDuQG1323149 at yorick.bic.mni.mcgill.ca>
>
> Hi,
>
> The way it is done in the cortical surface extraction pipeline is to
> first correct t1 and t2 for non-uniformities using N3 in native space,
> then to use mritoself like this:
>
> mritoself -nothreshold -mi -lsq6 t2.mnc t1.mnc t2_to_t1.xfm
>
> No brain mask is used. I have yet to see a failed case with this
> approach, but I'm sure it can fail. Easy to try.
>
> Claude
>