Hello
 
When I attempt to run brain extraction through BioImageSuite on
Windows XP I get the error below. I have followed the manual
installation instructions, added BET to the path, and saved the image
I am working on within BioImageSuite. Can you advise how to address
this?
 
Thank you
 
David Alexander Dickie
Brain Research Imaging Centre, Edinburgh
 

can't read "fname": no such variable
can't read "fname": no such variable
   while executing
"pxtclutil::Warning "The current image has not been saved\n as $fname
does not exist!\n Canceling $operation!" "
   (object "::pxitclbaseimageviewer::pxitclbrainstrip0" method
"::pxitclbrainstrip::EnsureCurrentImageIsSaved" body line 15)
   invoked from within
"$this EnsureCurrentImageIsSaved "Brain Segmentation" "
   (object "::pxitclbaseimageviewer::pxitclbrainstrip0" method
"::pxitclbrainstrip::RunBET" body line 3)
   invoked from within
"::pxitclbaseimageviewer::pxitclbrainstrip0 RunBET 1 "
   invoked from within
".pxtclobj11.viewer1.pxitclbrainstrip0.notebook.canvas.notebook.cs.page4.cs.bar2.h.1
invoke"
   ("uplevel" body line 1)
   invoked from within
"uplevel #0 [list $w invoke]"
   (procedure "tk::ButtonUp" line 24)
   invoked from within
"tk::ButtonUp .pxtclobj11.viewer1.pxitclbrainstrip0.notebook.canvas.notebook.cs.page4.cs.bar2.h.1"
   (command bound to event)

Two things that could be wrong:

1. Is the image saved to disk. Since BET is an external process you need to save the image first
2. Does the image filename contain spaces? If it does this can cause trouble.

Xenios

Thank you Dr Papademetris. The image was saved on a network drive; saving the image to the local drive resolved the problem.
 
Cheers
 
David

Excellent. Some of these issues are so tough to trace, so it is good to get lucky once in a while.

Xenios