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Today's Topics:
1. A Question about Spherical Registration (Reza Rajimehr)
2. Re: A Question about Spherical Registration (Donna Dierker)
----------------------------------------------------------------------
Message: 1
Date: Wed, 21 Feb 2007 02:25:17 -0500 (EST)
From: "Reza Rajimehr" <[EMAIL PROTECTED]>
Subject: [caret-users] A Question about Spherical Registration
To: caret-users@brainvis.wustl.edu
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain;charset=iso-8859-1
Dear caret-users,
I did the spherical registration of an individual human brain to the human
PALS atlas. I used the following dataset as the target atlas brain:
http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499
A new deformed .spec file has been generated. However, it has only one new
surface, which is a deformed sphere. I would like to visualize the
functional activities of the individual brain on the atlas brain (e.g. on
the atlas flat map). Should I download a more elaborate PALS dataset and
add them to the current directory? If so, should I redo the spherical
registration, or the new PALS surfaces (e.g. inflated, flattened, ...)
will be automatically linked to the deformed spherical surface that I
already have?
Thanks,
Reza
********************************
Reza Rajimehr, MD
NMR Athinoula A. Martinos Center
Department of Radiology
Massachusetts General Hospital (MGH)
Building 149, 13th St.
Charlestown, MA 02129
Email: [EMAIL PROTECTED]
********************************
------------------------------
Message: 2
Date: Wed, 21 Feb 2007 07:39:45 -0600
From: Donna Dierker <[EMAIL PROTECTED]>
Subject: Re: [caret-users] A Question about Spherical Registration
To: "Caret, SureFit, and SuMS software users"
<caret-users@brainvis.wustl.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=iso-8859-1; format=flowed
Hi Reza,
The atlas target dataset you used was the right one, but it is a
stripped down version that minimizes the number of files that get
deformed from the atlas to the individual's directory. (Some people
want to look at the atlas paint or border files on their individual's
surface, so then you would need to put those files in the atlas target
directory and add them to your atlas spec file; then, they would
automatically deform to the individual's directory during registration.)
Since you want to visualize on the atlas target, there's no need to
re-register; rather, just download one or more of these datasets:
PALS_B12.LEFT.STANDARD-SCENES.73730.spec
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595803
PALS_B12.RIGHT.STANDARD-SCENES.73730.spec
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595827
There are quite a few other options/documents listed here:
CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/directory.do?id=6585200
You can move your deformed results to the extracted directory, or move
the extracted files to your atlas target directory -- your choice. I
tend to create separate right and left subdirectories under my atlas
target directory, which has lots of files, but when I run registration I
use the single parent atlas target directory.
Often, we want to do group analysis of functional (metric) or anatomical
(surface_shape) data; in these cases, we create composite metric or
depth files. This command line utility (caret_command -help-full) can
be helpful:
caret_command -metric-or-shape-composite
caret_command -metric-or-shape-composite-named-column
If you're going to use the tools under Attributes: Metric and Surface
Shape Statistical Operations, then the spec files above lack the
distortion metrics and OPEN topo files included in these analysis datasets:
* Visualization/Analysis spec LEFT:
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6486316
* Visualization/Analysis spec RIGHT:
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6486393
Most of the tests can be run using the caret_command utility.
Donna
On 02/21/2007 01:25 AM, Reza Rajimehr wrote:
> Dear caret-users,
>
> I did the spherical registration of an individual human brain to the human
> PALS atlas. I used the following dataset as the target atlas brain:
>
> http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499
>
> A new deformed .spec file has been generated. However, it has only one new
> surface, which is a deformed sphere. I would like to visualize the
> functional activities of the individual brain on the atlas brain (e.g. on
> the atlas flat map). Should I download a more elaborate PALS dataset and
> add them to the current directory? If so, should I redo the spherical
> registration, or the new PALS surfaces (e.g. inflated, flattened, ...)
> will be automatically linked to the deformed spherical surface that I
> already have?
>
> Thanks,
> Reza
>
> ********************************
> Reza Rajimehr, MD
>
> NMR Athinoula A. Martinos Center
> Department of Radiology
> Massachusetts General Hospital (MGH)
> Building 149, 13th St.
> Charlestown, MA 02129
>
> Email: [EMAIL PROTECTED]
> ********************************
------------------------------
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