BrainVISA

Actually if possible can I upload this file and have someone look at it? I trimmed the volume some in the Z direction and ran an outside non-uniformity correction and it ran without error, but the final hemi surfaces are garbage. Every thing is fine with the pipeline until it gets to the hemi cortex...

Also, when trying to execute the histogram analysis from the command line, I get a "cannot open this file" error, even though the file -is- there and can be viewed in anatomist.

When I open the log window I don't see any command I can copy/paste to the commandline? Do you mean pick through it and re-create the command or is there another version of the log file I'm unaware of?

Thank you

Hi, I have a fairly normal, high contrast volume with no obvious defects that produces the following error, any idea what I can do to correc this? Process Ana Do A Lot of Things from T1 MRI 2 started on 2006/05/22 15:27 in Vip Histogram analysis 2 SignalException: System call interrupted with signal...

I have it all working now... The missing step was using the red magnifying glass instead of the file folder icon when importing the data.

Thanks for all the help!

Has anyone experienced this error before? Any work around? ------------------------------ ! VIP Warning: Risky regularization, gray matter to close to 0, skip! ------------------------------ ------------------------------ ! VIP Warning: Something was wrong with the iterative erosion! ---------------...

The section on databases gives me some generic information about "You should setup a database, it follows some defined set of rules", but it never defines what those rules are. If I just choose a folder as a 'database' in the menu, it does nothing. Even if I do this, import the data (with ...

That's why I'm confused, I've used the previous version (Maybe a year old?) and never had to create a database, or run any import step.

I'm unsure what you mean. I read up on teh database section, etc etc This does not sound like what I'm looking for. In the previous recent version of brainvisa, I could prepare subject for the pipeline, then run the pipeline. It would generate the output filenames based upon the input filename. Now ...

If I put in all of the output file names, it works

but is this supposed to be how it is or is there a way to have it automatically put in output file names based on the input file?

Thanks again

Nope it's a video card problem. I have it working now on another machine

from lspci:
01:05.0 Display controller: 3DLabs GLINT R3 [Oxygen VX1] (rev 01)

It is the video card, I tried it on another machine and the problem isn't there, although there is a different one (see brainvisa forum)

I'm getting the following error when tryign to execute the pipeline. I've already done "Prepare image for pipeline", and it was executed successfully. Not sure what to do since histo_analysis is supposed to be output Exception: argument histo_analysis is mandatory neuroProcessesGUI.py (870...

The GUI loads ok, I can use anatomist to view volumes, etc.

But whenever a "Run Process" is clicked, Python GPFs

This occurs in anything in which anatomist is launched to show a volume. as an example, prepare subject for anatomical pipeline Filetype is analyze, Anatomist opens fine, it shows a transaxial slice, everything seems "fine" but once the slider is moved to change the slice, either by draggi...