Hi Tim,
Here were the peaks in the params file you uploaded:
Human.icbm.L.params_file_20.2006-02-06.params:CGMpeak=127
Human.icbm.L.params_file_20.2006-02-06.params:WMpeak=156
Here are saner peaks that results in the nice segmentation in the
attached file:
Human.icbm.L.params_file_22.2006-02-06.params:CGMpeak=59
Human.icbm.L.params_file_22.2006-02-06.params:WMpeak=70
I know your lab prefers fully automated processes, but I'm afraid this
is a step where SureFit still requires user interaction; it has a big
impact on segmentation quality. This page might be helpful:
http://brainvis.wustl.edu/help/peak_tweaking/
Also, the bottom of the temporal lobe got cropped off. If you register
your anatomicals to an atlas space before segmenting, then you can use a
standard set of cropping parameters that gets rid of most of the
contralateral hemisphere without shaving off frontal/occipital petalia
and other cortical extrema.
Donna
On 02/06/2006 01:27 PM, Tim Jarvis wrote:
Donna / John,
I've uploaded the files to the site (left cropped AFNI volume, the spec and
param files)
The histogram peaks are correct, I used my own volume not the one from the
tutorial.
Thank you!
On 6 Feb 2006, Donna Hanlon wrote:
Hi Tim,
I don't come across this error very often, but I recall once seeing it
when the user had the WMpeak and GMpeak way too high; too low; or too
close to each other. The tutorial tells you what peaks to use. Did you
use GMpeak=57 and WMpeak=106?
Donna
On 02/06/2006 01:01 PM, John Harwell wrote:
Tim,
If you upload you volume file (header and data file) and the
".params" file we can try to determine the problem.
Upload your files at http://pulvinar.wustl.edu/cgi-bin/upload.cgi and
send us an email after you have uploaded the files.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
On Feb 6, 2006, at 12:24 PM, Tim Jarvis wrote:
Hi,
I'm following the tutorial, import my volume, set ac, crop, save, etc.
But upon doing the Surfit Operations / Segmentation, I get this error:
ERROR: In
/home/john/caret_linux/packages/src/VTK-4.2.3/Common/vtkImageData.cxx,
line 1566
vtkImageData (0x979fd80): GetScalarPointer: Pixel (-1, -1, 0) not in
memory.
Current extent= (0, 84, 0, 189, 0, 124)
Segmentation fault
This happens on both the Windows and Linux versions
Any ideas?
Thanks
---------------------------------------
Timothy R. Jarvis
---------------------------------------
Graduate Research Assistant
International Neuroimaging Consortium
VA Medical Center
612-467-2619
http://www.neurovia.umn.edu
---------------------------------------
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---------------------------------------
Timothy R. Jarvis
---------------------------------------
Graduate Research Assistant
International Neuroimaging Consortium
VA Medical Center
612-467-2619
http://www.neurovia.umn.edu
---------------------------------------
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