[MINC-users] am i using mincresample correctly

[Soren Christensen]

I just realized you ma have trouble using the composite view in
register if one or more of your volumes is 4D. At least for me, a 4D
volume will not render correctly in the composite view. You can work
around it by slicing out a single frame and doing away with the time
dimension using mincreshape. (eg -dimlenght time=0,0)

Soren

On Tue, Aug 7, 2012 at 10:26 PM, Andrew Janke <a.janke at gmail.com> wrote:
> 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.
>
>
> a
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