[MINC-users] Building xfm2def

[Andrew Janke]

Hi Andrew,

I took a quick look at this and something is amiss. If I add a -double
argument to the xfm2def line I get something much closer to what I'd
expect. My guess is that there is a data discretisation issue afoot.

If memory serves me correctly at some stage grid volumes for
non-linear transforms changed from short to double due to issues like
this and addition of small errors when making MDA's. Perhaps this has
something to do with it.

Can you file a issue for this in minc-toolkit?

Thanks


a


On 3 March 2016 at 22:43, Andrew Wood <andrew at biospective.com> wrote:
> Hi Andrew,
>
> I didn't open the grid directly, but rather showed what happened after
> applying it to a 3D volume.
>
> Instead of passing parameters to xfm2def to control the grid output, I used
> make_phantom parameters to make my data match xfm2def's defaults. Here's
> what I mean:
>
> $ xfm2param -rotations 30 30 30 ./rotations.xfm
> $ xfm2def ./rotations.xfm ./grid.mnc
> $ vim ./grid.xfm    # write an xfm for the deformation field
>
> $ mincinfo ./grid.mnc
>     dimension name         length         step        start
>     --------------         ------         ----        -----
>     xspace                    100            1          -50
>     yspace                    100            1          -50
>     zspace                    100            1          -50
>     vector_dimension            3      unknown      unknown
>
> $ make_phantom -xstart -50 -ystart -50 -zstart -50 -xstep 1 -ystep 1 -zstep
> 1 -xnelements 100 -ynelements 100 -znelements 100 ./phantom.mnc -xcenter 0
> -ycenter 0 -zcenter 0
>
> $ mincresample -transformation ./grid.xfm phantom.mnc phantom_rotated.mnc
> -use_input_sampling
>
>
> Here is the phantom, and the rotated phantom:
>
> https://drive.google.com/file/d/0BzcZlhs8X1gFZkZuSUtWRkFxcHM/view?usp=sharing
>
>
> Best,
> Andrew
>
>
>
> On Thu, Mar 3, 2016 at 12:38 AM, Andrew Janke <a.janke at gmail.com> wrote:
>
>> Hi Andrew,
>>
>> This should be fine for xfm2def, which component of the vector field
>> are you viewing in register? X?  The use case you describe is exactly
>> what it was written for.
>>
>> You generally have to specify a large number of input parameters to
>> xfm2def (start, step, nelem) in order to get what you want output.  I
>> thought there was a version floating around in which I implemented a
>> -like option but a quick search would say that I'm wrong.
>>
>>
>> a
>>
>>
>> On 3 March 2016 at 15:14, Andrew Wood <andrew at biospective.com> wrote:
>> > Hi again,
>> >
>> > I managed to build xfm2def (I'll issue a small pull request to update for
>> > VIO), but I'm not sure what to make of it's behaviour. I'm trying to use
>> it
>> > to approximate a linear transform as a deformation grid.
>> >
>> > I ran xfm2def on a "-rotations 30 30 30" xfm, then used it in
>> mincresample
>> > to rotate a make_phantom volume (grid and phantom sampled like each
>> other).
>> > Here's the result:
>> >
>> >
>> https://drive.google.com/file/d/0BzcZlhs8X1gFWUNQa2RMd3o3dTg/view?usp=sharing
>> >
>> > Are there limitations in xfm2def that would prevent it from
>> approximating a
>> > linear transform like this?
>> >
>> > Thanks,
>> > Andrew
>> >
>> > On Wed, Mar 2, 2016 at 11:38 PM, Andrew Wood <andrew at biospective.com>
>> wrote:
>> >
>> >>
>> >> Hi all,
>> >>
>> >> It looks like minctools isn't currently configured to build xfm2def. I
>> >> tried adding it to the CMakeLists.txt, but I'm getting errors:
>> >>
>> >> minc-toolkit-v2/minctools/progs/xfm/xfm2def.c: In function ‘main’:
>> >> minc-toolkit-v2/minctools/progs/xfm/xfm2def.c:96:4: error: unknown type
>> >> name ‘progress_struct’
>> >>     progress_struct progress;
>> >>     ^
>> >> ...
>> >>
>> >> Is there a reason that it's not part of the standard build? If not, is
>> >> there an easy way to add it? Or will it require development to bring it
>> in
>> >> line with the latest version of the libraries?
>> >>
>> >> Thanks,
>> >> Andrew
>> >>
>> > _______________________________________________
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