[MINC-users] averaging displacement -> black slices

[Audette, Michel]

Dear Andrew, 

thanks for the kind and prompt reply. Makes perfect sense! I have not looked at Oliver's script recently, but it would nice if it were that. 

Cheers,

Michel




-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Andrew Janke
Sent: Wed 7/4/2007 2:00 PM
To: MINC users mailing list
Subject: Re: [MINC-users] averaging displacement -> black slices
 
On 7/4/07, oliver.gress at medizin.uni-leipzig.de
<oliver.gress at medizin.uni-leipzig.de> wrote:
>
> I'm registering histological slices (minc volumes with z-depth=1) with
> hierarchical non-linear fitting using minctracc. I register each slice
> to its predecessor and successor. I get two minc files for the
> displacement volumes, which I average by mincaverage.
>
> My problem now is that after applying the averaged displacement to the slices
> by mincresample, almost every second slice just contains 'zero'-values, so
> they appear black. The problem seem to be the averaged displacement volumes
> because some of them work and some of them don't. All the displacement
> volumes are non-zero, so I wonder if the averaging can produce values that
> cause problems for the mincresample operation.

Hi Oliver,


My guess would be that you are getting displacements in the "z"
direction or at least the direction that is perpendicular to the
slices.  When you then transform the data this wil result in black
holes as the data is moved out of the plane. Are you setting the
deformation in this direction to 0?


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883
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