Automatic segmentation into Brodmann Areas

Questions about Anatomist manipulation

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houenou
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Automatic segmentation into Brodmann Areas

Post by houenou »

Hello,
Is there a way to get an automatic segmentation of a T1-image with Anatomist ? I mean, a segmentatin of the brain into Brodmann Areas which would define different Brodmann areas as differents ROI ?
Thanks
Josselin HOUENOU
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Jean-Francois Mangin
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Post by Jean-Francois Mangin »

NO,
I would say this kind of tools does not exist anywhere...
However, some people do an approximation of it using spatial normalization. You have a normalized Brodmann atlas you backproject
on your MRI. See SPM list or freesurfer list.
houenou
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Post by houenou »

Thanks. At least is there a software which could automatically segment specific regions of the brain like amgdala or hippocampus ?
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Jean-Francois Mangin
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Post by Jean-Francois Mangin »

houenou wrote:Thanks. At least is there a software which could automatically segment specific regions of the brain like amgdala or hippocampus ?
As far as I know, there is somesthing like that plugged into Anatomist by Marie Chupin from the LENA
Manik
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Post by Manik »

There is also a Brainvisa version of Marie Chupin's work (I did it with her), but I am not sure about the distribution of this package. You can ask her directly by using the private messaging function on this forum, for the user marie chupin. Just click on "pm" on this page :
http://brainvisa.info/forum/profile.php ... file&u=139
Manik Bhattacharjee
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skesler
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Re: Automatic segmentation into Brodmann Areas

Post by skesler »

Does anyone have updated info on Marie Chupin's plugin or know of a protocol for automated hippocampus segmentation/measurement? I have been unable to track this down or find any information on how to conduct such an analysis. Thanks for your help.
joost
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Re: Automatic segmentation into Brodmann Areas

Post by joost »

Hi,

if you´re looking for hippocampus segmentation software outside BrainVisa i suggest you have a look at FSL-FIRST.

best,
-joost
Manik
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Re: Automatic segmentation into Brodmann Areas

Post by Manik »

Hi,

you can ask Marie directly about her software, I know she is still improving her program and the brainvisa processes.
I will send you her address through a private message,
Manik Bhattacharjee
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binarybottle
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Re: Automatic segmentation into Brodmann Areas

Post by binarybottle »

I enjoyed reading Marie Chupin's ISBI 2008 paper: "Fully automatic hippocampus segmentation discriminates between early Alzheimer's disease and normal aging" -- very nice work. The results seem to be competitive with the following published fully automated hippocampus segmentation software packages:

1. S. Powell et al. / NeuroImage 39 (2008) 238–247

2. Morra, et. al. NeuroImage Volume 43, Issue 1, 15 October 2008, Pages 59-68

3. Vanderlijn et al. Hippocampus segmentation in MR images using atlas registration, voxel classification, and graph cuts. Neuroimage (2008) vol. 43 (4) pp. 708-720

I would be very interested to evaluate Marie Chupin's approach as well for use in our research here at Columbia University. Could you please put me in touch with Ms. Chupin? (my email address is arno[at]binarybottle.com)

Cheers,
@rno

arno klein
asst. professor of clinical neurobiology
columbia university
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Yann Cointepas
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Re: Automatic segmentation into Brodmann Areas

Post by Yann Cointepas »

Hi Arno,

I sent an email to Marie with a link to your message.

Best regards,

Yann Cointepas
binarybottle
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Re: Automatic segmentation into Brodmann Areas

Post by binarybottle »

Thank you, but I still haven't heard back from Marie Chupin. Is there someone with whom I can discuss this application of BrainVISA? Again, I would be interested in evaluating the software for possible use by our imaging laboratories.

cheers,
@rno
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