[MINC-users] am i using mincresample correctly

[Jackie Leung]

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.

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.

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.

Any advice will be very much appreciated!!

Jackie

On Sun, Aug 5, 2012 at 8:57 AM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Jackie,
>
> On 5 August 2012 10:44, Jackie Leung <jackie.leung at alumni.utoronto.ca>
> wrote:
> > I'm new to MINC and I'm not sure if my coregistration process is correct.
> >
> > After getting the transform file from 'register', I apply it to my
> volumes
> > (it's a 4D dataset) with the following command:
> > mincresample -transformation matrix.xfm -tfm_input_sampling data.mnc
> > data_reg.mnc
> >
> > when i view the output data using register, it looks the same as before.
> > I'm I running the tool correctly?  Or does it have something to do with
> the
> > world coordinates vs voxel coordinates thing?
>
> My guess is that you have actually done the right thing. Just remember
> that register displays volumes in "voxel space" and
> -tfm_input_sampling will in general just change the voxel to world
> transform in a file. If you want to resample a file like another (the
> target) you probably want this:
>
>    mincresample -transformation matrix.xfm -like target.mnc data.mnc
> data_reg.mnc
>
> An explanation of what is going on is here:
>
>    http://en.wikibooks.org/wiki/MINC/Tools/mni_autoreg
>
> This is for minctracc, but the resampling section still applies.
>
>
> a
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