[MINC-users] minctracc on 2D volumes?

[Soren Christensen]

Hi Paul,
 Adding to that, you may want to try padding with two all-zero slices in
each z-extreme (on top of what Mallar suggested).
I had to do that to force and in-plane registration only. It was a tip from
Andrew.

Cheers
Soren

On Thu, Jul 14, 2011 at 6:31 PM, Mallar Chakravarty
<mallar.chak at gmail.com>wrote:

> Hi Paul,
>
> It’s tricky to get minctracc to work on 2D slices in linear mode.  I would
> suggest using the -w_translations and -w_rotations options that you
> basically “turn off” the out of plane components by using an absurdly small
> value.
>
> mallar
>
> On Thu, Jul 14, 2011 at 3:00 AM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca
> >wrote:
>
> > Dear all,
> >
> > Would anyone know if it is possible to run minctracc on 2D minc volumes?
> >
> > I am running some 2D simulations in different orientations and I would
> like
> > to estimate some transformations using minctracc (I would like to avoid
> the
> > need to create 3D volumes if possible). I have tried it but to no avail,
> > i.e. the output xfm file contains nan values (please see below for
> output).
> >
> > Any suggestions would be greatly appreciated.
> >
> > Best Regards,
> >
> > Paul
> > ______________________________**___
> >
> > [2D_MINC] 218% minctracc -clobber -mi -lsq6 xtrue_rot45deg.mnc
> > xtrue_target_0deg.mnc xtrue_45deg2_0deg.xfm
> >
> > COG of v1: -0.800728 3.766018 0.000000
> > COG of v2: 3.196798 2.931377 0.000000
> >   [trans] = 3.997526 -0.834641 0.000000
> > WARNING: source volume not UNSIGNED_BYTE, will do conversion now.
> > WARNING: target volume not UNSIGNED_BYTE, will do conversion now.
> > out :     nan=F     nan=F  1.5000=T    1.0000=T  1.0000=T  1.0000=T
> > 0.0000=T  0.0000=T  0.0000=T
> > out :     nan=F     nan=F  1.5000=T    1.0000=T  1.0000=T  1.0000=T
> > 0.0000=T  0.0000=T  0.0000=T
> > out :     nan=F     nan=F  1.5000=T    1.0000=T  1.0000=T  1.0000=T
> > 0.0000=T  0.0000=T  0.0000=T
> > out :     nan=F     nan=F  1.5000=T    1.0000=T  1.0000=T  1.0000=T
> > 0.0000=T  0.0000=T  0.0000=T
> > out :     nan=F     nan=F  1.5000=T    1.0000=T  1.0000=T  1.0000=T
> > 0.0000=T  0.0000=T  0.0000=T
> > out :     nan=F     nan=F  1.5000=T    1.0000=T  1.0000=T  1.0000=T
> > 0.0000=T  0.0000=T  0.0000=T
> > out :     nan=F     nan=F  1.5000=T    1.0000=T  1.0000=T  1.0000=T
> > 0.0000=T  0.0000=T  0.0000=T
> > out :     nan=F     nan=F  1.8491=F    1.0000=T  1.0000=T  1.0000=T
> > 0.0000=T  0.0000=T  0.0000=T
> > out :     nan=F     nan=F  1.6164=F    1.0000=T  1.0000=T  1.0000=T
> > 0.0000=T  0.0000=T  0.0000=T
> > out :     nan=F     nan=F  1.4418=T    1.0000=T  1.0000=T  1.0000=T
> > 0.0000=T  0.0000=T  0.0000=T
> > out :     nan=F     nan=F  1.6164=F    1.0000=T  1.0000=T  1.0000=T
> > 0.0000=T  0.0000=T  0.0000=T
> > out :     nan=F     nan=F  1.4418=T    1.0000=T  1.0000=T  1.0000=T
> > 0.0000=T  0.0000=T  0.0000=T
> > out :     nan=F     nan=F  1.5000=T    1.0000=T  1.0000=T  1.0000=T
> > 0.0000=T  0.0000=T  0.0000=T
> > Initial objective function val = 10000000000.00000000
> > Final objective function value = 10000000000.00000000
> >
> > [2D_MINC] 221% xfm2param xtrue_45deg2_0deg.xfm
> > after parameter extraction
> > -center         0.00000    0.00000    0.00000
> > -translation        nan        nan        nan
> > -rotation           nan        nan        nan
> > -scale              nan        nan        nan
> > -shear              nan        nan        nan
> >
> > [2D_MINC] 222% mincinfo xtrue_rot45deg.mnc
> > file: xtrue_rot45deg.mnc
> > image: signed__ short -32768 to 32767
> > image dimensions: zspace yspace xspace
> >    dimension name         length         step        start
> >    --------------         ------         ----        -----
> >    zspace                      1     -1.21875           -0
> >    yspace                    256      1.21875     -155.391
> >    xspace                    256      1.21875     -155.391
> >
> > [2D_MINC] 223% mincinfo xtrue_target_0deg.mnc
> > file: xtrue_target_0deg.mnc
> > image: signed__ short -32768 to 32767
> > image dimensions: zspace yspace xspace
> >    dimension name         length         step        start
> >    --------------         ------         ----        -----
> >    zspace                      1     -1.21875           -0
> >    yspace                    256      1.21875     -155.391
> >    xspace                    256      1.21875     -155.391
> >
> > ______________________________**_________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-users<
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users>
> >
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