[MINC-users] minctracc with mask: objective function starts at0.0: what to do?

[Audette, Michel]

Hi Andrew, 

thanks for your kind reply. 

What I am doing, is using a mask to weight an affine transformation to part of an anatomy. For example, I make a mask that coincides with a facial nerve, a 2nd mask that coincides with the ear-drum, and so on. In all of these cases, I want to use a global affine transform, for the whole inner ear, as a starting point for a piecewise affine registration, where one piece is the nerve, another is the ear-drum and so on. I am in fact registering a source of micro-MR, from which the Robert Funnell inner ear model is derived, to high-res patient CT, in order to insert the components of the Funnell model in patient data. 

So it isn't mask to mask per se. Also, the mask was in fact dilated with mincmorph (8 successive dilations), in relation to the tight shape that I had. Still getting a null objective function when I try the piecewise. 

minctracc -model_mask facialPatchedD8_xyz_rightear_mi_affine_flip9.mnc -mi -w_translations 0.16 0.16 0.16 -w_rotations 0.0028 0.0028 0.0028 -step 0.64 0.64 0.64 -transformation HumanS16885_Stack_nuc_xyz_rightear_mi_affine_9.xfm HumanS16885_Stack_nuc_xyz_res_rigid.mnc.gz etzold_emma_12792115_003002_mri_xyz.mnc HumanS16885_Stack_nuc_xyz_rightear_mi_affine_facialMask9.xfm -clob -lsq6

Does your solution still apply, do you think? 

Cheers, 

Michel

-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Andrew Janke
Sent: Fri 1/18/2008 3:31 PM
To: MINC users mailing list
Subject: Re: [MINC-users] minctracc with mask: objective function starts at0.0: what to do?
 
Hi Michel,

I presume you mean you are aligning a mask to another mask?  If this
is the case yes you will have a fairly "saturated" objective function.

I would suggest using something like mincmorph and do a distance
transform on both of them and then align that.

The other option would be a mincblur with a big FWHM.

good luck


a

On Jan 19, 2008 12:27 AM, Audette, Michel
<Michel.Audette at medizin.uni-leipzig.de> wrote:
> Hi folks,
>
>
>
> I'd like to try to use some anatomically shaped (and morphologically dilated) masks to refine an affine registration into a piecewise affine registration. I'm seeing however that my objective function with minctracc starts off with a null objective function, for middle ear registration, and therefore produces the same transformation as its starting point. Is it possible to make its computation a bit more sensitive than it is?
>
>
>
> Cheers,
>
>
>
> Miche
>
>
>
> Michel Audette, Ph.D.
>
> Innovation Center Computer Assisted Surgery (ICCAS)
>
> Semmelweisstraße 14
>
> Leipzig, Germany
>
> Phone: ++49 (0) 341 / 97 - 1 20 13
>
> Fax: ++49 (0) 341 / 97 - 1 20 09
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-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

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