[MINC-users] minctracc and cropped images

[Oliver Gress]

Hi Simon,

in my case, I used -w_rotations 0 0 1 to set the rotation around x- and y-axis 
to zero and it worked, so I always got something like
-rotation       0.00000    0.00000    0.01142
I wonder why you get rotations (your "-rotation" output is from xfm2param, 
right?). A look into the minctracc manual tells, that the weights are set for 
the optimization. In my understanding it means that no rotation should be 
estimated. Perhaps someone from the BIC knows more exactly how the weights 
are incorporated in the optimization. I'm sorry that I can't help you better.

To your other problem, if it is a one-time task, you could manually find an 
initial translation (and perhaps scaling) and create an initial 
transformation (param2xfm) that you can feed to minctracc with 
"-transformation <file.xfm>", but then you probably could also build a coarse 
mask. And without a mask, I could imagine that the objective function (i.e. 
the default crosscorrelation) could give better values when the subset is in 
some way stretched to cover a great part of the full set.

I hope that helps a little

Oliver


On Thursday 22 November 2007 13:34, Simon Fristed Eskildsen wrote:
> Hi Oliver,
>
> Thanks for the quick reply.
> If the weights are 0 the optimization will still be able to change the
> rotations, right?
>
> In any case, with -w_rotations 0 0 0, I get:
> -rotation      -0.84230   -0.25758   87.84906
>
> where default is:
> -rotation      -3.17860   -8.78379   80.04449
>
> I will try with a mask, but my problem is that I have no way to estimate
> the size of the mask used for the target, as I only know that my source
> is a subset of my target (not how big a subset).
>
> Simon
>
> Oliver Gress wrote:
> > Hi Simon,
> >
> > I think the easiest way is to use "-w_rotations 0 0 0". It sets the
> > weights for rotations to zero for the optimization, so no rotation will
> > be present in the estimated transformation.
> > To exclude parts of a volume from the estimation, you can set masks for
> > the target and source volumes with "-model_mask <filename>" and
> > "-source_mask <filename>". I think the mask files are binary minc files,
> > so coordinates of your MRI volumes that fall into regions of zero value
> > in the mask files will not be used for the optimization of the objective
> > function.
> >
> > Best regards
> > Oliver
> >
> > On Thursday 22 November 2007 12:17, Simon Fristed Eskildsen wrote:
> >> Hi all,
> >>
> >> I have a number of bitmap images. Each image is a coronal slice from a
> >> T1 MRI. Using rawtominc I have managed to create a minc volume from the
> >> bitmaps.
> >> I have the original scan in dicom, which I have converted to minc using
> >> dcm2mnc.
> >> Now I would like to align my volume created by rawtominc (let's call it
> >> "bitmap volume") with the original scan. However, the bitmap volume is
> >> cropped compared to the original scan, and minctracc does not seem to do
> >> a very good job aligning the two volumes. Is there a way to let
> >> minctracc know that the source does not have to match all of the target?
> >> Also, I don't need rotations in the transformation. Is there a way to
> >> force minctracc to not use rotations, only translations and scale?
> >>
> >> Thanks,
> >> Simon
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
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