Hi Joanna,
See inline replies below.
Donna
On 11/08/2007 11:49 AM, Joanna Hutchison wrote:
Hello,
I am a new Caret user, and I am a bit confused by a couple of things that I am hoping can be easily clarified.
First, we use Linux as our primary computer operating system. In the Linux environment, I am getting Caret files to load, but the images are either not visible at all or they are distorted in some fashion.
I use the Linux version with no problems. Questions:
* How old is your caret version (from the header bar int the main window?
* Which Linux version do you use (if RedHat, do "cat /etc/issue" at
command line)?
* What kind of graphics card do you have?
When I use Caret in Windows, this problem disappears; however, I need to use the Caret-AFNI interface, and AFNI does not operate in a Windows environment.
Few people (any?) use this feature anymore, for two reasons:
* AFNI and SUMA are more tightly integrated (e.g., volume and surface
palette and thresholding).
* Caret now includes volume visualization features, so you can click in
the volume, jump to the surface, and vice versa.
You can view your AFNI volumes directly using Caret, without need for
the AFNI interface, which may no longer work.
Do you know of a program, a patch, or the like, that will allow the Caret images to appear appropriately when used in the Linux environment? Alternatively, do you know of a way to interface the Windows version of Caret with AFNI that is running in Linux?
When I import MPRAGE files from AFNI into Caret in the Linux environment using your directions in the segmentation tutorial, however, the images actually look fine and I am able to crop the brain nicely. When the brain segmentation process begins, however, it inevitably fails.
If you upload the volume (NIFTI or .HEAD/.BRIK pair) you are trying to
segment, I'll have a look:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
Tell me which peaks you used. Upload the spec file, too.
It appears that when the parameters for voxel size are adjusted to the required
size, the image is degraded and the program can no longer distinguish between
white and gray matter sufficiently,
Caret doesn't resample on its own; you can do it explictly using Caret's
Volume: Edit volume attributes: data tab, or preprocess in AFNI. Nothing
Caret does during segmentation should degrade image quality.
though this is just an educated guess as to what is happening. I had thought
that ANFI would automatically size the voxels appropriately, but it apparently
does not do so. Is there a remedy for this problem, or am I committing a fatal
error somewhere? Is it possible that this problem is a result of our scan
resolution as opposed to an AFNI-Caret problem? (I think that our scan
resolution is fairly standard, so I suspect this not to be the case.)
After you upload the volume, I'll have a much more concrete picture of
the problem.
Thank you very much for your time and your help. I am looking forward to using
Caret as soon as we get these kinks worked out. It is a very impressive program.
Cheers,
Joanna Hutchison
--------------------------------------------------------------
Joanna Hutchison, Ph.D.
Department of Psychiatry-University of Texas Southwestern Medical Center
School of Behavioral and Brain Sciences-University of Texas at Dallas
Center for BrainHealth-University of Texas at Dallas
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