[MINC-users] minctracc on 2D volumes?

[Mallar Chakravarty]

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>
>