[MINC-users] am i using mincresample correctly

[Andrew Janke]

Hi Jackie,

On 7 August 2012 13:00, Jackie Leung <jackie.leung at alumni.utoronto.ca> wrote:
> Thank you for the responses.  I am now fairly convinced that the transform
> did take effect, but as Andrew said, I just don't see it using register.

Soren has answered this part pretty comprehensively already.

> Now this has led me to a second problem.  I wish to convert the registered
> data into nifti format using mnc2nii, but this method doesn't seem to keep
> my world coordinates, thus defeating the whole registration process.

mnc2nii does put this world to voxel transformation into the Nifti
header. Unfortunately for your various packages out there treat this
transformation differently. Some even ignore it completely.

> I did try the -like option in mincresample, and that does work in
> transforming the voxel space as well.  However, it also crops a significant
> portion of my data as my target image has a lot fewer slices.
>
> So, is there a way to apply a transform to the voxel space (not just world
> space) while keeping the original field of view?  or another option would
> be if mnc2nii can apply the world coordinates to the nifti output instead
> of voxel space.

I think you have two options.

1. resample the partial volume (the one with a lower resolution) to
the higher one. You currently seem to be going in the other direction.

2. As Soren mentioned define the sampling you want and resample to that.


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