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help > RE: BrainAligner : displacement field
Aug 8, 2011 03:08 PM | Hanchuan Peng
RE: BrainAligner : displacement field
I guess there is a new bug about
theparsing of -t and -F. I can take a look when I find
time.
However, even myself do not really use the DF directly (unless several years ago). It is just an intermediate step for warping. Can you tell me why you need it, instead of directly aligning brains?The BrainAligner program does not accept the DF as an input, thus even you have it you won't be able to directly use BrainAligner and the DF file to do warping. Instead, what you need is the pair of landmark files output by the program, the DF will be computed based on the pair of landmarks directly ...
-hanchuan
Originally posted by Thomas Templier:
However, even myself do not really use the DF directly (unless several years ago). It is just an intermediate step for warping. Can you tell me why you need it, instead of directly aligning brains?The BrainAligner program does not accept the DF as an input, thus even you have it you won't be able to directly use BrainAligner and the DF file to do warping. Instead, what you need is the pair of landmark files output by the program, the DF will be computed based on the pair of landmarks directly ...
-hanchuan
Originally posted by Thomas Templier:
Hello Hanchuan,
thank you for the update. Unfortunately, I can't make it work properly. I would like to obtain the displacement field for the global transformation and then for the warping. In both cases I get the normal outputs but I fail having the DF as output.
This sentence in the help bothers me :
Secondly, if I run BA with the same parameters as I did before, everything works well but I get the weird warning :
Let me know if you need some logs.
Thank you.
Best Regards
Thomas
thank you for the update. Unfortunately, I can't make it work properly. I would like to obtain the displacement field for the global transformation and then for the warping. In both cases I get the normal outputs but I fail having the DF as output.
This sentence in the help bothers me :
Note: specify -t will disable -F even -F
is specified.
It means that the only way to have the DF is to omit -t, and give
the input and output landmarks to compute the DF. If I omit -t like
this :./BA -s subject.tif -L
landmarks_target.csv -l landmarks_subject -B 1024 -H 2 -c 1 -w 10
-o output.tif -F DF.raw
then I have the message :You have not specified the target image.
Do nothing.
If I omit -t and -s, I have the message :You have not specified the subject image
or the outpuf image. Do nothing.
I've also tried this without success :./BA -t target.tif -s subject.tif -L
landmarks_target.csv -B 1024 -H 2 -c 1 -w 10 -o output.tif -F
DF.raw
Secondly, if I run BA with the same parameters as I did before, everything works well but I get the weird warning :
The data is not with a TIF surfix, -- now
this program assumes it is RAW format defined by Hanchuan
Peng.
Let me know if you need some logs.
Thank you.
Best Regards
Thomas
Threaded View
| Title | Author | Date |
|---|---|---|
| Thomas Templier | Jul 10, 2011 | |
| Hanchuan Peng | Jul 11, 2011 | |
| Thomas Templier | Jul 12, 2011 | |
| Hanchuan Peng | Jul 13, 2011 | |
| Thomas Templier | Aug 5, 2011 | |
| Hanchuan Peng | Aug 6, 2011 | |
| Thomas Templier | Aug 8, 2011 | |
| Hanchuan Peng | Aug 8, 2011 | |
| Thomas Templier | Aug 8, 2011 | |
| Hanchuan Peng | Aug 9, 2011 | |
| Thomas Templier | Aug 9, 2011 | |