[MINC-users] minctracc and cropped images

[Oliver Gress]

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