background_val

[Alexandra Cunliffe]

Hi,

I'm having trouble with the command "background_val" in my command
file. With this command, I am trying to set all pixels in the output
image without a specified value to -10000. Specifically, I would like
the border of the image and the top and bottom slices to have values
of -10000 when areas of the scan to be registered do not exist in
these locations. However, my output images often have a border and top/
bottom slices with 0 HU pixels. The default background pixel value is
supposed to be -999, so I'm not sure why I am seeing this. My mhd file
for a simple example is below. Maybe you could tell me if I am
misusing or misunderstanding this command?

Also, I just updated plastimatch, so I am using the most current
version.

Thank you,
Alex Cunliffe

# command_file.txt
[GLOBAL]
fixed=/fixed.mhd
moving=/moving.mhd
img_out=out.mhd
xform_out=/xform_out.mhd

[STAGE]
xform=translation
optim=rsg
max_its=30
res=10 10 5
background_val=-10000

[STAGE]
xform=translation
optim=rsg
max_its=100
res=4 4 2
background_val=-10000

[Paolo Zaffino]

Dear Alexandra,

for the border issue I solved using the matlab function "delete_edges.m"
that you can find into the extra/matlab plastimatch directory.
If you prefer there is a way to do this using python (that is free).
Anyway check always the results, because this is only a "patch" (the
code assumes that the registration is fine).

For the other one problem I don't know...I have never used that feature,
I'm sorry.

Hope this helps.
Regards.

Paolo

[Sharp, Gregory C.]

Hi Alex,

Regarding the failure of background_val, this seems to be a bug.
Should be an easy fix, but we should wait until Tony finishes the
code reorganization.

Another possible workaround is to create the xform, then warp afterward
using "plastimatch warp" with --default-value option.

Greg

Dear Alexandra,

Hope this helps.
Regards.

Paolo

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[Alexandra Cunliffe]

Thanks for the options!
Would you mind alerting the group when the code reorganization is
finished?

Thanks!
Alex

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[Sharp, Gregory C.]

Hi Alex,

I made the fix.

If you are on linux, you can probably update and try. Windows is still
kind of iffy. I advise to save a copy of your existing build before
trying the update.

[Alexandra Cunliffe]

Hi,
Thanks for letting me know. I just tried updating and had a few problems, so I'm not sure if the fix was actually installed on my computer. The output from the update is below. Currently, I am at revision 3654, and running plastimatch version 1.5.4-beta (2737)

When I perform registration, I still encounter the same issue. I specify background_val=-10000 in the parameter file, but the borders of the scan have 0 values.

Output from update:
make
[  1%] Built target lbfgs
[  2%] Built target bstrlib
[  3%] Built target devillard
[  3%] Built target nocedal
[ 13%] Built target lua_library_static
[ 13%] Built target specfun
[ 16%] Built target plmsys
[ 42%] Built target plmbase
[ 53%] Built target plmutil
[ 54%] Built target plmclp
[ 56%] Built target plmdose
[ 66%] Built target plmregister
[ 69%] Built target plmsegment
[ 71%] Built target plmreconstruct
[ 74%] Built target plmscript
Linking CXX executable ../../../landmark_warp
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libreadline.so: undefined reference to `tgetstr'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libreadline.so: undefined reference to `tputs'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libreadline.so: undefined reference to `BC'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libreadline.so: undefined reference to `tgetent'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libreadline.so: undefined reference to `tgetflag'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libreadline.so: undefined reference to `tgoto'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libreadline.so: undefined reference to `UP'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libreadline.so: undefined reference to `tgetnum'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libreadline.so: undefined reference to `PC'
collect2: ld returned 1 exit status
make[2]: *** [landmark_warp] Error 1
make[1]: *** [src/plastimatch/cli/CMakeFiles/landmark_warp.dir/all] Error 2
make: *** [all] Error 2

[Sharp, Gregory C.]

Hi,

Your plastimatch update didn't compile, so that's why you
don't see the new behavior for background_val. Specifically, when
you see the version is (2737), that is the SVN revision.

I did some web searching, and it looks like it's possible that
you need to install the following packages:

libtermcap and libtermcap-devel

then, re-run cmake and give it another go.
(Not sure if this will work, so keeping my fingers crossed...)

-Greg

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[Alexandra Cunliffe]

Hi Greg,

We have the packages that you mentioned already installed.

It looks like the problem may actually be that there is no linking to the ncurses library. When I add -lncurses to link.txt in landmark_warp.dir, this part compiles with no problem. I'm getting the same error later on for plastimatch.dir, bragg_curve.dir, and maybe others.

Thanks!
Alex

On Wednesday, June 13, 2012 12:22:18 PM UTC-5, Sharp, Gregory C. wrote:

Hi,

Your plastimatch update didn't compile, so that's why you
don't see the new behavior for background_val.  Specifically, when
you see the version is (2737), that is the SVN revision.

I did some web searching, and it looks like it's possible that
you need to install the following packages:

libtermcap and libtermcap-devel

then, re-run cmake and give it another go.
(Not sure if this will work, so keeping my fingers crossed...)

-Greg

________________________________

[Sharp, Gregory C.]

Hi Alex,

 

I think I could fix it.  Do you mind updating and trying again?

 

Thank you,

Greg

---

From: plast...@googlegroups.com [mailto:plast...@googlegroups.com] On Behalf Of Alexandra Cunliffe
Sent: Thursday, June 14, 2012 3:42 PM
To: plast...@googlegroups.com
Subject: Re: [Plastimatch] Re: background_val