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Please post more details as to exactly

1. Which version did you download?
2. The exact command-line.
3. What version of Ubuntu are you running?
4. The error message itself.

Xenios

Hello, can you please help me to install in Ubuntu? I am using the given command, sh ./bioimagesuite_[filename].sh in the terminal and I am only receiving errors.

Thanks a lot.

This is the second public beta release of BioImage Suite 3.0 (beta2 was
never made publicly available.). This has been in development for about
18 months and in internal testing at the Yale MRRC since the beginning of
2009. It is still meant as a preview/testing release and not for
``production'' work at this stage -- handle with care, although it is
getting closer to official release status.  This is release is a major update to 3.0beta1
(see the release announcement for that at
http://research.yale.edu/bioimagesuite/forum/index.php?topic=308.0
which was released in May of 2009.)

A good description of the architecture/design of BioImage Suite 3 can be found at  http://bioimagesuite.org/talks/bis3_talk.pdf

To download see the instructions at: http://research.yale.edu/bioimagesuite/forum/index.php?topic=173.msg1020

The direct download link is: http://bioimagesuite.org/download/Install_beta.html

In addition to complete source code we provide binary releases for:

* Linux 32-bit
* Linux 64-bit
* MS-Windows (native, VS2008)
* MS-Windows (MSYS)
* Mac OS X 10.4 or later (intel)
* Mac OS X 10.4 or later (powerpc)

BioImage Suite is supported in part by the NIH/NIBIB under grant R01 EB006494.

Cool. Thanks.

Yes -- feel free to eliminate it in setpaths. In the 3.0 beta this is changed (I should be up tomorrow, we are testing the installers today)

Xenios
 

Xenios,

   It appears that the scripts that set the paths for BioImage Suite still automatically set the FSLDIR variable to the "default value" which according to the setpaths.csh file is ANALYZE. In the newest version of FSL this output is no longer supported and ANALYZE cannot be set as one of output options in the fsl.csh file. I am having some issues running any tool in FSL and I am wondering if BIS's automatic setting of the FSL output variable in the usr/local/fsl path is what is causing my problem. The BET tool in BIS also doesn't work and it appears to be the same problem. My fsl.csh file is set to have NIFTI_GZ as the default output type. Do we just have to get rid of this variable in the BIS setpaths.csh if I am using the newest FSL release or am I doing something wrong?

Hope all is well.

                                                                                                           -Gad

This is now online see the main BioImage Suite webpage.

XP

We have posted the updated version of our "VTK" book (updated to VTK 5.2). You can find this (including all code examples etc.)
at http://www.bioimagesuite.org/vtkbook5/index.html.

BioImage Suite 3.0beta3 (beta 2 was never publicly released next) -- we are making small tweaks at this point.

Xenios

As Xenios mentioned, ictal SPECT has a high success rate (upwards of 90%) in localizing the lobe of seizure onset. The success rate drop very quickly when looking for more specific regions. Thus we generally only want to find big blobs in a single lobe when we do this analysis. Smoothing allows this by effectively lowers the resolution. You can see this effect on the sample dataset from spect.yale.edu by lower the smoothing kernel in the SPECT tool. As the kernel becomes smaller, we get less of a big blob and more of small islands through out the brain.

Dustin

Usually the SPECT image quality in this context is not high enough to permit localization to anything other than "lobe", smoothing effectively lowers the resolution.

XP