Hi Julia, plus others interested in registering surfaces (FreeSurfer-
as well as SureFit-generated) to the PALS human atlas,
John and Donna have already provided useful technical comments that
have hopefully addressed the specific questions you raised.
This email provides a heads-up on two
John,
It sounds like your best bet would be to use border contours to
outline the 2nd and 3rd activations. You can do this using Surface:
Region of Interest Operations: Operate on Selected Nodes: Operation:
Create Borders Around Clusters.
Start by selecting the nodes of interest for the
Katrin,
You can also improve resolution by increasing the size of the main
Caret window. In photoshop you can then adjust the dpi.
David VE
On Mar 26, 2007, at 8:42 AM, John Harwell wrote:
Hi,
We tell the software that writes the image to write the image in
the highest quality possible
Hamied,
The best source I know of for your questions is the CoCoMac database
developed by Rolf Kotter and colleagues.
http://cocomac.org/home.htm
You have to get an account, but once you do, you can search for
connections of any area of interest and then click on the area
abbreviation to
Rishi,
A couple of points to add to Donna's.
1) The 'Core 6' landmarks refer specifically to human cortex, not the
macaque. The calcarine sulcus has a rather different configuration
in the macaque (especially in posterior regions).
2) If your objective is to make a calcarine cut to reduce
Reza,
On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote:
Dear caret-users,
David Van Essen suggested me to use the following .deform_map file for
deformation of macaque F99 to Human PALS:
RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-
LDMK-VE.73730.spec.deform_map
Once y
Reza,
On Feb 16, 2007, at 3:48 AM, Reza Rajimehr wrote:
We have done an fMRI experiment in macaques and humans. The
anatomicals of
macaques and humans have been fully reconstructed in FreeSurfer. The
functionals have been also analyzed in FreeSurfer/FS-FAST. We have
successfully imported som
Leon,
I can replicate and explain your observations in the following way:
1) Load a foci file that contains data in multiple stereotaxic
spaces, and view the foci with the FLIRT average fiducial surface in
the main window.. At this stage, each focus will be in its original
space, even tho
Leon,
On Dec 9, 2006, at 7:59 AM, Leon Deouell wrote:
Thanks again for your help. I am making nice progress. My questions
now are:
1. Is it possible to see the foci on volume slices? It seems I can
only see
them on surface files.
Yes - Use File: Open Data File: Open Foci File - Volumes (*
Mateus,
First, it is important to clarify whether your request pertains to
nodes (as stated) or to foci. In Caret terminology, nodes refers
specifically to the points that make up a surface and have locations
specified within a coordinate file. Foci refers to stereotaxically
identified
John,
On Nov 13, 2006, at 11:26 AM, John Arsenault wrote:
Hello,
Firstly I found that I got a better segmentation with the .35mm
isotropic voxels relative to the same volume resampled to .5mm
isotropic.
Good to know.
Secondly I am having a bit of trouble registering an
individual hemisph
Dear Dr. Labus,
To begin on a general note, we are very keen to promote exactly what
you're doing - putting stereotaxic-coordinate data (foci) into Caret
(and as a next step into SumsDB for public access). Hence, we want
to make sure that this tutorial actually works for investigators like
John,
On Nov 2, 2006, at 9:38 AM, John Arsenault wrote:
Hello,
I have an anatomical image taken at .35mm isotropic. For some
reason I
was under the impression that one should resample there data to .
5mm for
registration with the F99 surface. Is this true or is this only for
data of res
Graham,
I'll let John and/or Donna comment next week on the brainfish
questions you raise. This algorithm was originally developed in Ted
DeYoe's lab, and I'm not aware that it has been used extensively by
others since incorporation into Caret.
Regarding conversion of metric files to tex
Graham,
On Oct 26, 2006, at 11:37 PM, Graham Wideman wrote:
.
Good! The issue of whether the average fiducial surface
intersects various blobs of activation is an important one. [...]
Right -- that all sounds good. What I'm not yet convinced about
intuitively is that the average surf
Shawn,On Oct 26, 2006, at 3:12 PM, Shawn Mikula wrote:thanks Donna, but I was looking for something closer to the attached images.Shawnhttp://sumsdb.wustl.edu/sums/directory.do?id=6585200&dir_name=CARET_TUTORIAL_SEPT-06Click the brain icon next to Macaque.F99.RIGHT.STANDARD-SCENES.73730.specSelect
Graham,
On Oct 26, 2006, at 6:35 PM, Graham Wideman wrote:
Donna:
> All the PALS_B12 surfaces are mid-cortical thickness surfaces.
Hmmm, this will send us on a closer inspection of the surfaces in
conjunction with volumes.
I think we've been somewhat disoriented at looking at an average
To current and prospective Caret users,
John Harwell and I will be giving a demonstration of Caret 5.5,
SumsDB, and WebCaret at the INCF neuroinformatics booth (# 2728) on
Tuesday, October 17th (9:30 - 12:30). If you are interested and have
a moment, please stop by. If you know of colleag
Jason,
Donna's suggestions are worth following, though I must admit that I
have not personally used the Draw Borders, type Closed, Assign Voxels
to Within Closed Border option, so I don't know quite how it will
behave for your purposes.
Another option to consider is to use the Surface: RO
John (et al.),
I guess Donna wins a six-pack, because I do indeed have a response.
1) First, some general comments. Your questions come at a propitious
time.
We are just completing a major revamping of the macaque F99 atlas
along with many other changes to the macaque and human (PALS) atla
John,
1) We had a problem last spring in which the then-current version of
Caret5 was hanging when I tried to run the flat deformation
process. The problem you have encountered may well be different,
but I would nonetheless suggest that you try downloading the latest
version of Caret an
David,
John's suggestion should work (I think). Another option that will
work, albeit indirectly, is to generate an 'RGBpaint' file by way of
a metric file as an intermediary.
Use the surface: ROI option to select nodes in one of your paint
ROI's. Then use ROI: Operation: Assign metric
Terry,
I've experienced this problem before and found the following work-
around:
Translate the flat map so that its coordinates are entirely positive
(if you want to save right hemisphere foci) or entirely negative (if
you want to save left hemisphere foci). Then project the foci to the
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