[MINC-users] minctracc on 2D volumes?

[Claude LEPAGE]

Hi Paul,

I have demonstrated the capabilities of minctracc to run
in 2D mode on histology slices (volume N x M x 1 - 1 slice
thickness) in linear and non-linear mode. You need your
slice to be in x,y plane, account for weights and lattice
size in z-direction, and finally mincblur in 2D. If I recall,
don't include shear (lsq12) in your linear registration. The
rest works. Shear may work too but I haven't figured it out
completely. You need to give a non-zero (+ve ??) voxel 
thickness in the z-direction and have the 2 slices at the 
same z start. Seems that the latter is done.

Perhaps you can drop by my office next time you go breathing
at the corner of BTRC. :-) We'll try it out on your demo mnc
file below.

Claude

> 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
>
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