AimsMorphoMath?

SylvainT · Post by **SylvainT** » Fri Jul 21, 2006 2:39 pm

hi there,
I'm looking for this program, which appears in the list of aims commands ( http://brainvisa.info/doc/html/shfjcomm ... mands.html ) but doesn't seem to be included in brainvisa 3.0.1 or 3.0.2
thanks,
sylvain

SylvainT · Post by **SylvainT** » Fri Jul 21, 2006 2:43 pm

ok, I guess I can try NmrMorphologicalOperation...
sorry for posting a bit too early

SylvainT · Post by **SylvainT** » Fri Jul 21, 2006 3:03 pm

okokok... now, I've tried that Nmr program... I'm just trying to do a closing on a binary image (a head mask created by BV)... can anybody help me with the options?

1. it asks for a threshold and a threshold mode, which I don't know what they are...

2. it gives me an error "invalid output type" when I try to run it

thanks,
sylvain

denghien · Post by **denghien** » Tue Jul 25, 2006 8:56 am

Hi,

We have the same pb at SHFJ !

Code: Select all

denghien% AimsMorphoMath-2006_07_21
QFile::open: No file name specified
/home/appli/Fedora-4/SHFJ_pack-main-linux-2006_07_21shfj-1/bin/commands-links/AimsMorphoMath: No such file or directory

Otherwise, there are 2 other commands: AimsOpening and AimsClosing.

I suppose that NmrMorphologicalOperation is a command which do a lot of things ... threshold, opening, closing .... if you want just to do a closing, I think that you must use the -op closing and -r options.

About "invalid output type", I know that sometimes it is better to convert your data in S16.

Isa

Post by **riviere** » Tue Jul 25, 2006 12:56 pm

Hi,
Well, I think there is a little bit of mix-up in the commands.html web page, and commands that are not in the stable release have been listed here. Sorry.
AimsMorphoMath doesn't exist in the current release: it is a new command, only in the development version.
You can use AimsErosion, AimsDilation, AimsClosing and AimsOpening for standard morphomath operations on binary volumes.
Denis

SylvainT · Post by **SylvainT** » Wed Jul 26, 2006 3:18 pm

okok, thanks!

but there's a little problem with AimsClosing... the usage (result of 'AimsClosing -h') says it computes the Chamfer distance map; it's actually identical to what you get when you do 'AimsChamferDistanceMap -h'... bug?

(you can see this in the commands.html file also

)

Denis, can you give me the true usage for AimsClosing... I suspect it's the same as AimsOpening, but a confirmation would be nice! thanks!

Post by **riviere** » Wed Jul 26, 2006 3:26 pm

Hmm, yes you're right: AimsClosing description is wrong. However the arguments doc is OK because they are automatically generated from what the command actually expects.
Denis

SylvainT · Post by **SylvainT** » Wed Jul 26, 2006 4:18 pm

yep, I just tried it and it seems to do what it's supposed to! thanks!

Jean-Francois Mangin · Thu Jul 27, 2006 2:08 pm

If you get some more trouble, try the MorphoMath
commands of Vip, Aims ones mainly stem from them
and maybe some have not been tested enough...
Be careful however, the Vip I/O do not follow the help of the commandline,
they are the Aims Ones (add the extension .ima to the image name)