Hi!
I have been playing a bit more with the misalignment between the
cortical surface and the MRI in the left hemisphere of the macaque data
set released in January 2004. I have replaced the original HEAD files
with the attached ones and I am relatively happy with the results.
CAUTION: These files should only be applied to the left hemisphere, not
to the right one!
Best,
Jochen.
David Van Essen wrote:
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
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USA
office: +1 (530) 754-5084
lab: +1 (530) 754-6987
fax: +1 (530) 757-8827
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_______________________________________________
caret-users mailing list
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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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