Hello Sarah,
Thanks very much.
Venkateswaran
-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Sarah Andersen
Sent: Thu 2/24/2011 10:47 AM
To: [log in to unmask]
Subject: Re: [FSL] A question on atlases
Hi Venkat,
The threshold is the value that the probablistic atlas has be thresholded
at. For example, thr25 would only show areas that correspond to the given
structures in 25% or greater of the atlas population. The names
corresponding the colors are in an xml file that is found in the atlas
folder. Just look at the intensity value of the color in fslview and find
the corresponding label index in the xml file. Note that the xml file starts
at 0, and I believe the intensity values start at 1, so you may need to
subtract one from the intensity to get it to line up.
Hope this helps,
Sarah
On Thu, Feb 24, 2011 at 8:08 AM, Rajagopalan, Venkateswaran <
[log in to unmask]> wrote:
>
> Dear All,
>
> I did VBM analysis and now I am looking at my results. I used cluster and
> atlasquery to get coordinates and corresponding regions of the brain. For
> visualization purposes I tried to overlay Harvard cortical atlas (in FSLview
> over MNI 2mm brain and my tstat file) so I saw a folder named atlases in my
> FSL directory and inside this I have a Harvard cortical atlas folder inside
> of it there are files ending with......thr25-2mm etc like that. I would like
> to know what these thresholds mean and when I choose one of them I have a
> colored atlas I am wondering is there a way get the names of different
> regions of brain pertaining to different colors in the atlas.
>
> Thanks
>
> Venkat
>
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--
Sarah Andersen
Research Specialist
University of Arizona
Dept. of Speech, Language, and Hearing Sciences
(520) 621-9877
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===================================
P Please consider the environment before printing this e-mail
Cleveland Clinic is ranked one of the top hospitals
in America by U.S.News & World Report (2010).
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.
Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed
and may contain information that is privileged,
confidential, and exempt from disclosure under applicable
law. If the reader of this message is not the intended
recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are
hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited. If
you have received this communication in error, please
contact the sender immediately and destroy the material in
its entirety, whether electronic or hard copy. Thank you.
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