Hi Dr. Smiley,
Correct: If you've somehow generated a surface from your anatomical MRI
outside of Caret, then you'll likely be able to import it into Caret to
display it. In most cases, you also can flatten and register it, as
well, but there can be problems drawing borders on surfaces generated by
methods other than SureFit. In any case, Caret can almost always
display the volume.
As for creating surfaces, there already is a caret version that will
generate an initial segmentation from an anatomical volume. The problem
is that there usually are many handles in it, so you need something like
SureFit's automatic error correction to fix most of them, and then
manually patch the residual ones. Patching is already easier in Caret
with the Segmentation: Find Handles feature, but the automatic error
correction algorithm still needs to be integrated into Caret. (The code
has been ported from python to C++, though.) Then there are some
remaining user interface issues (e.g., cropping, setting peaks) that
need to be addressed.
I'm hoping we might have an alpha version late March with beta in late
April. Time will tell if this is just wishful thinking on my part.
This seems like about the fifth time I've gotten this question in the
last two days. I've been meaning to post an update on the
caret-users/caret-announce list.
Donna
On 02/22/2005 09:34 AM, Smiley, John wrote:
Thanks for your response.
I have both histological sections and MRI. Am I correct to understand that
Caret will display, but not create, the 3d surface from and anatomical volume?
The tutorial says future versions of Caret will be able to create surfaces.
Any speculation how how far away that is?
John Smiley
-----Original Message-----
From: [EMAIL PROTECTED]
To: Caret, SureFit, and SuMS software users
Sent: 2/21/2005 12:12 PM
Subject: Re: [caret-users] importing images
Hi Dr. Smiley,
If the files are numbered like 00001.tif, 00002.tif, ..., 00099.tif,
then you can do this on the command line:
cat *tif > my_monkey.raw
Then, you can import monkey.raw as a Raw Volume file. You'll need to
know the dimensions (z will be # of tif files) an the datum type.
You'll be able to view this volume in Caret, but if you want to generate
a 3d surface from the anatomical volume, you'll need to do this in
SureFit, which is not available on MacOSX yet.
If these tiff files are, say, histological sections rather than MRI
scans, then have a look at Caret 4.6 tutorial 10
(http://brainmap.wustl.edu/caret/pdf/CARET_UsersGuide.03-06.Part-II.pdf)
.
We haven't yet generated a Caret 5.1 version of this tutorial, but I
believe the same functions are available in Caret 5.1.
Donna
On 02/21/2005 10:14 AM, Smiley, John wrote:
Hi:
I'm newly using Caret on Macintosh OSX. I would like to import a 3d
volume (monkey brain) that is in a stack of consecutive Tiff files.
Could someone suggest a way to reformat these images for importation
into Caret?
Thanks,
John Smiley
---
John Smiley, Ph.D.
Program in Cognitive Neuroscience and Schizophrenia
Nathan Kline Institute for Psychiatric Research
Orangeburg, NY
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