open-discussion > Brain extraction error
Showing 1-4 of 4 posts
Sep 14, 2011 10:09 AM | David Alexander Dickie
Brain extraction error
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)
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)
Sep 14, 2011 03:09 PM | Xenophon Papademetris
Brain extraction
error
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
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
Sep 14, 2011 04:09 PM | David Alexander Dickie
RE: Brain extraction error
Thank you Dr Papademetris. The image was saved on a network drive;
saving the image to the local drive resolved the problem.
Cheers
David
Cheers
David
Sep 14, 2011 04:09 PM | Xenophon Papademetris
RE: Brain
extraction error
Excellent. Some of these issues are so tough to trace, so it is
good to get lucky once in a while.
Xenios
Xenios