Jochen,
On Oct 13, 2005, at 6:50 PM, Jochen Ditterich wrote:
Thank you, David. I probably have been using older files than the ones
you have pointed me to, but there is one thing I don't understand.
When I go to the SumsDB home page (without logging in, just public
access), select the Atlases directory, and select the MACAQUE
directory I basically have access to the following two files:
MACAQUE.LEFT_HEM.04-01-29.tar.gz and
MACAQUE.RIGHT_HEM.04-01-29.tar.gz. These are the files I have been
working with and I have always assumed that these are the latest
releases of the macaque data sets.
They were the latest back in January 2004, as indicated by the date in
the filename. However, there are many more recent macaque atlas files
in SumsDB.
One data set in particular is an updated right hemisphere macaque
atlas; this should be the current starting point for getting data files
of interest. This is the
Macaque.F99UA1.Cerebral.RIGHT.ATLAS_SCENES.35946.spec:
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6413561 in the
ROOT /public /ATLAS_DATA_SETS /MACAQUE/ directory. As the name
indicates, it incorporates 'scene' files that facilitate viewing in
both Caret and WebCaret.
When searching for the newer files you have pointed me to individually
I can find them. Is there a complete archive available like the ones I
have been using so far containing all necessary files or do I have to
download them separately and figure out which ones belong together?
Your questions are very sensible, and they point to the reality that we
are still chipping away at getting our 'atlas house' in better order.
Thus, we have a newer scenes-based atlas file for the macaque right
hemisphere, but not yet one for the left. Basically, this is because
we are multi-tasking on many atlas and other fronts; it is a challenge
to keep the atlas datasets reasonably current for human, macaque, rat,
and mouse in the face of software refinements along with additional
data that is good to bring into the atlas framework.
Feedback from the user community helps us prioritize what aspects are
most useful to concentrate on.
David
David Van Essen wrote:
Hi Jochen,
On Oct 13, 2005, at 4:58 PM, Jochen Ditterich wrote:
Hi Donna and John,
I was running into a strange observation when using the "Surface
Outline" function in Caret's MRI viewer. When applying it to your
macaque cortex datasets there seems to be a relatively substantial
misalignment between the MRI and the layer 4 surface model,
especially for the left hemisphere. Have you noticed this before
or
am I doing something wrong?
There are multiple versions of the macauqe fiducial surface and the
volume data in SumsDB, and not all of them are properly aligned with
one another.
The relevant data files are accessible from the Atlases directory,
along the top row of the SumsDB home page. Select the MACAQUE/
directory
(http://sumsdb.wustl.edu/sums/directory.do?
dir_id=679531&dir_name=MACAQUE), then the hemisphere(s) you want. You
can then view the data in WebCaret and download what you like.
Alternatively, you can directly download the following two surfaces
and one volume that should be well aligned:
Macaque.F99UA1.LR.03-11+orig.HEAD
http://sumsdb.wustl.edu:80/sums/archivelist.do?id=6413573
Macaque.F99UA1.Cerebral.L.FIDUCIAL.AC_origin.34132.coord
http://sumsdb.wustl.edu:80/sums/archivelist.do?id=685724
Macaque.F99UA1.Cerebral.R.FIDUCIAL.AC_origin.04-01-23.35946.coord
http://sumsdb.wustl.edu:80/sums/archivelist.do?id=686089
I generated screen shots from a combination that is well aligned, but
it got put on hold by the Caret 'moderator' because of image size.
That version will presumably be distributed tomorrow, but in the
meantime this is the text-only response.
Let us know if alignment problems persist or if there are other
issues that arise.
David VE
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Jochen Ditterich, Ph.D.
Assistant Professor
Center for Neuroscience
University of California
1544 Newton Court
Davis, CA 95616
USA
office: +1 (530) 754-5084
lab: +1 (530) 754-6987
fax: +1 (530) 757-8827
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