I am a fairly new user of BioImage Suite. The configurations I am presently using are:
BioImage 3.0
Linux 2.6.32-52-generic x86_64 GNU/Linux

The problem I am facing is, whenever I try to load CT or MR image in Brain Register, the Brain Register window closes abruptly. This continues for an uncertain number of times till it somehow manages to hold and properly open the images for registration. In times, I have had to try opening the files around 30 times! before I successfully manage to open them.

Anyone knows how to work around this problem?

Thanks,
Piyush R.
Johns Hopkins

Piyush,

What Linux are you on? This way we can set up a virtual machine on our end with the same distribution and try to replicate.

Thanks!

Xenios

Originally posted by Xenophon Papademetris: As I mentioned, I am using
Linux 2.6.32-52-generic x86_64 GNU/Linux

or

Linux Lucid 10.04 64bit version.

Sorry for the confusion.

A quick test revealed a bug in one of the tcl scripts. I attach a fix, please replace bis_colorblendimage.tcl in bioimagesuite30/bis_algorithm with this one and let me know how it goes.

Xenios

Just confirming, do you want me to replace the tcl script in bioimagesuite30_64/bis_algorithm ?

In the terminal I generally get the following message while starting bioimage
       BioimageSuite ready to run. Type bis.tcl to get the starting menu (/usr/local/bioimagesuite30_64)
       Loading unix /usr/local/bioimagesuite30_64/lib/libvtkpxCommonTCL.so

Also, can I know if there can be any errors if this tcl file does not function properly? Basically I would like to understand what this tcl file does, so that I know if anything goes wrong. Thanks.

Yes this is correct. The fix has to do with (preventing) an access to a NULL pointer in the Color Blend Module. Please check if, when you use this replacement script, the Brain Register application starts.

Xenios

No! 
It doesn't seem to have any improvements. I am also facing the same problem while using electrode editor window. 
Once I try to load the MR images, in closes abruptly few times before working as intended. 
The Bioimage Suite remains open, but both the windows which open when we click on "Electrode Editor"; close.
Similar is the case during registration. When we load CT ot MR images, the 3 windows which open when we click "Brain Register" close abruptly.
Regards,
Piyush

Hm. Can you run this from the command line and see if it reports any errors.

Open terminal
source /usr/local/bioimagesuite30_64/setpaths.sh
pxitclbrainregister.tcl

Also type ldd /usr/local/bioimagesuite30_64/setpaths.sh/libvtkpxCommonTCL.so and send me the output.

Thanks,

Xenios

reconstruction@rachmaninov:~$ source /usr/local/bioimagesuite30_64/setpaths.sh

BioimageSuite3_Base is now in your path
Key Components
/usr/local/bioimagesuite3_base64/cmake26/bin/cmake
/usr/local/bioimagesuite3_base64/tcl84/bin/tclsh
/usr/local/bioimagesuite3_base64/vtk52/bin/vtk
/usr/local/bioimagesuite3_base64/gdcm2/bin/gdcminfo
CLAPACK in /usr/local/bioimagesuite3_base64/clapack3
ITK in /usr/local/bioimagesuite3_base64/itk310/lib/InsightToolkit
MYSQL in /usr/local/bioimagesuite3_base64/mysql50
BioimageSuite ready to run. Type bis.tcl to get the starting menu (/usr/local/bioimagesuite30_64)
reconstruction@rachmaninov:~$ pxitclbrainregister.tcl
Loading unix /usr/local/bioimagesuite30_64/lib/libvtkpxCommonTCL.so
//                                                                                                                 [BRAIN REGISTER WINDOW OPENED PROPERLY HERE. NO ERROR]
^C
reconstruction@rachmaninov:~$ ldd /usr/local/bioimagesuite30_64/setpaths.sh/libvtkpxCommonTCL.so
ldd: /usr/local/bioimagesuite30_64/setpaths.sh/libvtkpxCommonTCL.so: No such file or directory

OS: Mac
Bioimage 3.0

Having similar problem as Piyush, but trying to do SPM with the Yale example images. Once I am running isas, y try to register images, but when I select TR Viewer after loading the images, the program abruptly shuts down, with the console showing:

error: xp_attach_gl_context returned: 2

I google this error and it appears to be associated with X11 (Xquartz). I deleted XQuartz and downloaded it again but still the same error.

I would really appreciate any help.

yamil

What Mac OS version are you on? What size are your images?

You may be having memory issues as the version we supply for Macs is 32-bit unfortunately.