users
users > RE: Warps settings optimization
Apr 18, 2016 03:04 PM | Greg Jefferis
RE: Warps settings optimization
Originally posted by Pieter Louwe:
-X [exploration] (default 16)
-G [grid-spacing] (default 40)
-E [energy] energy of warp transform (default e-1)
-J [0 to 1] jacobian-weight volume constraining param (default 0)
The metric can be set by:
-M [metric] (Supported values: nmi, mi, cr, msd, ncc, default is nmi)
You can get help for munger by choosing help for CMTK tool, running munger on the command line without arguments, or going to:
https://gist.github.com/jefferis/6cac924...
Best,
Greg.
Thank you for the quick and helpful reply. I had
a closer look at my data with your comments in mind, in most of
channel the registration is almost perfect. There are a few bits
where the registration isn't though. If i then look at these bits
in the affine registered data I noticed that in these cases the
structures where quite far apart. So it would appear that the
warping isn't able to bridge the gap and register all the
way.
In these cases, is is the whole volume that is not well aligned at
the affine stage, or just part of the volume? If the former, you
need to improve your initial affine estimate. If the latter then as
Torsten discusses you could increase the grid spacing/step size or
increase the ability of the registration to deform the volume
(principally warp energy). There is one either that might be worth
checking off the shelf – switching the metric to e.g. cross
correlation, since these images must be very similar.As you guessed correctly I am using the munger.
To loosen the warping should I be changing the values for Jacobian
constraint and rigidity weight then ? It would be great if Greg (
or anyone else) could give some advice on how to adapt the
munger.
eYou can change the following munger command line options to modify
the parameters discussed above.-X [exploration] (default 16)
-G [grid-spacing] (default 40)
-E [energy] energy of warp transform (default e-1)
-J [0 to 1] jacobian-weight volume constraining param (default 0)
The metric can be set by:
-M [metric] (Supported values: nmi, mi, cr, msd, ncc, default is nmi)
You can get help for munger by choosing help for CMTK tool, running munger on the command line without arguments, or going to:
https://gist.github.com/jefferis/6cac924...
Best,
Greg.
Threaded View
| Title | Author | Date |
|---|---|---|
| Pieter Louwe | Apr 16, 2016 | |
| Torsten Rohlfing | Apr 16, 2016 | |
| Pieter Louwe | Apr 18, 2016 | |
| Torsten Rohlfing | Apr 19, 2016 | |
| Torsten Rohlfing | Apr 19, 2016 | |
| Greg Jefferis | Apr 18, 2016 | |