On 01/16/2007 01:28 PM, Remya Nair wrote:
HI Donna, Thanks for the reply. Meanwhile I had gone through the
tutorial and have done the following:
Converted my images to afni format and then viewed them in Caret. They
look fine now. Since the afni header file has orientation and origin
info. is it right to assume that, the parameters for origin,
orientation etc. that show up in Volume Attributed Menu are
correct?Please confirm
Assuming your DICOM to AFNI conversion tool is well-behaved, then yes:
Both DICOM and AFNI contain the orientation and origin info Caret needs,
so all should be well.
I assumed they were correct and am presently trying to generate a
surface from my anatomical volume using segmentation. I have rescaled
my voxel size to 0.5 mm for macaque. Hwever, on doing this it gives me
the fooolwing error and the program aborts:
"Error in Hind Brain Segmentation."
What could be the reason for this.
A likely culprit is that your actual volume origin is far from the
anterior commissure. The Caret/SureFit routines that separate eye and
hindbrain depend on these constraints:
* The origin must be close to the anterior commissure.
* The volume must be approximately AC-PC aligned; if the head is rotated
too far up or down, or to the side, then you'll have problems like this.
Let's hope it's the origin, which is the easier problem to solve. If
your actual origin is far from the AC, then use Volume: Edit Volume
attributes to change the origin to the actual AC, but keep track of the
before and after origin positions, so you'll know the exact translation
parameters to use later, when you translate the resulting fiducial
surface to match your non-AC origin.
Thanks!
Remya
On Jan 16, 2007, at 2:07 PM, Donna Dierker wrote:
Hi Remya,
See inline replies below.
On 01/15/2007 01:36 PM, Remya Nair wrote:
Hi Donna
I am new to Caret, so any help would be greatly appreciated.
There are a number of things that I intend to do.
1. View macaque data sets in Caret. These are in Dicom format and so
I understand that they cannot be imported to Caret directly. Is that
true?
True, I'm afraid. I confess when I've needed to do this I've used 3rd
party converters (e.g., Freesurfer's mri_convert and AFNI's to3d).
I tried converting my data to Analyze format using "rDICOM2ANALYZE"
command and then importing the resulting file in Caret.
I'm not familiar with this command; I'm guessing it's your local
institution's conversion utility.
This displayed a small image in one corner of the Caret main window
and not the whole window. What am I doing wrong?
Probably nothing, but the Analyze format typically lacks origin and
orientation information that Caret needs. You can compensate for this
using the Volume: Edit Volume Attributes menu. If you don't know your
actual origin setting, then try using -xdim/2, -ydim/2, -zdim/2. At
least then, you will probably see something reasonable in the Caret
window.
2. Next, I want to register my anatomical to the F6 or F99 atlas.
How is this done?How do I specify my own "Origin" when I do this?
One way is to use Caret to segment your anatomical and then use
spherical registration to deform your macaque's surface to the F99
atlas. Another way is to use some third party volume registration
tool (e.g., FSL's flirt) to register your anatomical volume to the
atlas volume.
If you haven't already looked at this tutorial, there are sections on
the new macaque F6 atlas:
CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/directory.do?id=6585200
Before doing a lot of work, I'd at least scan the tutorial document.
Thanks in advance!
Caret Newbie
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Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see
http://home.att.net/~donna.hanlon for details.)
