[MINC-users] am i using mincresample correctly

[Jackie Leung]

OK, I tried using option 2...  that is, create a spatial template (if
that's the correct term) by expanding the FOV of the target data.  This is
the command I used:

mincresample target.mnc target_temp.mnc -xstart 30 -xnelements 250 -ystart
-50 -ynelements 250

then apply the transform to my data:

mincresample data.mnc data_reg.mnc -transformation matrix.xfm -like
target_temp.mnc

and it seems to work fine. Thank you Soren and Andrew for your advice.

I don't think I have the same issue with 4D data in register, but there is
one tiny thing I noticed. It appears that when I create target_temp.mnc,
the first slice of the first dynamic loses all its data and goes black.  I
even tried the simple command and got the same result:

mincresample target.mnc target_temp.mnc

This isn't a problem for my situation as the first data-point is not
necessary for my analysis anyways, but just wondering if this is some kind
of bug?

thanks,
jackie


On Tue, Aug 7, 2012 at 9:10 PM, Soren Christensen <sorench at gmail.com> wrote:

> 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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