Sarang,
1) You mention using hdr/img files which have limited metadata. When
viewing your MRI, press the "R" button in the toolbar. If the
crosshairs are over the anterior commissure things are okay. If the
crosshairs are not over the anterior commissure follow the procedure
in the segmentation tutorial and then save the volume as an AFNI volume.
2) If the AC is properly set and you are still experiencing the
memory problem, I would suggest downloading an updated version of
Caret available from "http://brainmap.wustl.edu/pub/john/";. Use
"pub" for the username and "download" for the password. Look for
files beginning with "caret5_exe". Unzip Linux and Windows versions
in your caret installations "bin" directory and Mac versions in your
caret installation's "apps" directory.
3) If you continue to run out of memory upload your volume to http://
pulvinar.wustl.edu/cgi-bin/upload.cgi. After doing so, send me the
name of your volume file(s).
----------------------------------------------------------
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 May 12, 2006, at 5:10 PM, Sarang S. Dalal wrote:
I'm trying to use the SureFit segmentation, and it always stops
with an out of memory message, both on my 1GB MacBook (intel Mac)
and 2GB Red Hat Linux workstation. I'm starting with a standard
human MRI in Analyze (hdr/img) format, with 1x1x1.5 mm (128 x 128 x
62 voxels). Then I defined the AC, rescaled to 8-bit (0-255),
resampled to 1x1x1 mm, and saved the output to a new hdr/img pair.
The SureFit segmentation proceeds for about 10 minutes, then stops
while either "Determining the inner boundary" or "Determining the
outer boundary" saying that Caret is unable to acquire more memory,
with a "Continue" button and an "Exit Caret" button. Indeed, at
this point, Caret has used up all available RAM plus roughly half
of the available swap space, with no other programs running.
Pressing the Continue button simply pops up the same box again,
while "exit caret" behaves as advertised.
I'm wondering if something is configured wrong on my installation,
or if there's something strange with my input MRIs. Please let me
know if there are any suggestions.
Thanks,
Sarang Dalal
_________________
/ \___________________
| Sarang S. Dalal \_______
| UCSF Biomagnetic Imaging Laboratory \
| UCSF/Berkeley Bioengineering Graduate Group )
| http://tempest.ucsf.edu/~sarang/ __________/
| [EMAIL PROTECTED] ______/
| +1.415.476.6888 _________/
\_________________/
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