[MINC-users] in plane

[Soren Christensen]

Hi,
 I am trying to correct some dynamic perfusion CT data for motion.
The slices are relatively thick at 12 mm and there are only 2 of them
so coverage is sparse. It seems the main components of the motion are
around the z axis so I am trying to constrain the registration to
in-plane rotations (that way there is some data left to analyze as
well).

I am not sure if there is any straightforward way to do this with the
MINC tools so I tried to add some lines to mritoself to pass through
w_translations and w_rotations to minctracc.

I would think that setting the following should achieve in plane
translations and rotations only
-w_rotations 0 0 0.017
-w_translations 1 1 0

But when I check the resulting xfm file that is not the case (verbose
listing from mritoself at the end of this mail):

xfm2param 18t00.xfm
after parameter extraction
-center         0.00000    0.00000    0.00000
-translation   -1.60969    0.41978   -0.04529
-rotation       0.00000    0.00000    0.50024
-scale          1.00000    1.00000    1.00000
-shear          0.00000    0.00000    0.00000

The rotation bit seemed to work - but not translation.
So where am I going wrong - and is there a way to do what I want?


Thanks,
Soren




Verbose output from mritoself:

pc-mugin /NEWCASTLE/mc_corr_tests# mymritoself -resample t.mnc
-w_rotations 0 0 0.0174533 -w_translations 1 1 0 -keeptmp -clobber
-far -verbose  -nothreshold frame18.mnc frame00.mnc 18t00.xfm


[mymritoself] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10
21:28:57] /usr/local/mni2/bin/autocrop -clobber frame18.mnc
/usr/tmp/mymritoself_16343//frame18_crop.mnc -step -0.4921875
-0.4921875 11.817999999999999616 -extend 0,0 0,0 0,0 -byte
[autocrop] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10
21:28:57] /usr/local/mni2/bin/mincreshape -clobber -byte frame18.mnc
/usr/tmp/mymritoself_16343//frame18_crop.mnc -start 0,0,-1 -count
2,512,513
Copying chunks:..Done.
[mymritoself] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10
21:28:57] /usr/local/mni2/bin/autocrop -clobber frame00.mnc
/usr/tmp/mymritoself_16343//frame00_crop.mnc -step -0.4921875
-0.4921875 11.817999999999999616 -extend 0,0 0,0 0,0 -byte
[autocrop] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10
21:28:57] /usr/local/mni2/bin/mincreshape -clobber -byte frame00.mnc
/usr/tmp/mymritoself_16343//frame00_crop.mnc -start 0,0,-1 -count
2,512,513
Copying chunks:..Done.
[mymritoself] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10
21:28:57] /usr/local/mni2/bin/minctracc -clobber
/usr/tmp/mymritoself_16343//frame18_crop.mnc
/usr/tmp/mymritoself_16343//frame00_crop.mnc
/usr/tmp/mymritoself_16343//18t00_tmp1.xfm -est_center
-est_translations -lsq6 -mi -groups 256 -w_rotations 0 0 0.0174533
-w_translations 1 1 0 -step 7.3 7.3 7.3 -simplex 10
COG of v1: 3.561098 -68.172920 -620.482849
COG of v2: 1.893397 -68.351616 -620.528137
   [trans] = -1.667701 -0.178696 -0.045288
Only center & trans required, now returning from init_transformation
Initial objective function val = -1.36852753
Final objective function value = -1.41425633
[mymritoself] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10
21:28:57] /usr/local/mni2/bin/minctracc -clobber
/usr/tmp/mymritoself_16343//frame18_crop.mnc
/usr/tmp/mymritoself_16343//frame00_crop.mnc 18t00.xfm -est_center
-transformation /usr/tmp/mymritoself_16343//18t00_tmp1.xfm -lsq6 -mi
-groups 256 -w_rotations 0 0 0.0174533 -w_translations 1 1 0 -step 4.3
4.3 4.3 -simplex 1.5
Initial objective function val = -1.41286337
Final objective function value = -1.41485536
[mymritoself] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10
21:28:58] /usr/local/mni2/bin/mincresample -clobber frame18.mnc t.mnc
-byte -transform 18t00.xfm -like
/usr/tmp/mymritoself_16343//frame00_crop.mnc
Transforming slices:..Done