[MINC-users] minctracc and cropped images

[Simon Fristed Eskildsen]

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
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