I personally like to look at the whole cluster, and do my best to be specific as to which regions (BA areas and basic anatomical locations) in which the cluster falls. I have often seen large clusters which can 'meander' through several regions, and clusters which link together at the edge but clearly cover multiple regions. I always think it is best to be specific and hate when researchers only report the localization of the peak.

Donald, is there a toolbox or function for labeling using AAL with percentages? I have tried an anatomy toolbox, which can be very useful, but it seems to have legacy versions of functions from SPM5 in its path, so when I install it it causes SPM8 to cease functioning.

Colin

On 17 March 2014 17:13, MCLAREN, Donald <[log in to unmask]> wrote:

Another point to consider, most researchers use the peaks to define the location, rather than the entire cluster.

They may miss regions if a region doesn't contain a peak OR if the analysis program only provides the top 3 peaks of the cluster.

Do you have a recommendation of how many regions you should list for your peak?

I have thought about using the AAL atlas and saying X% of the cluster is A, Y% in B, etc. This better characterizes the cluster, but doesn't use probabilities from probablistic atlases. I'd be open to suggestions to integrate probabilities into the percentages.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=====================
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.

On Mon, Mar 17, 2014 at 1:18 PM, Colin Hawco <[log in to unmask]> wrote:

For what it is worth, I would advise caution on any automated labelling system. Not all atlases are correct, and the labels, particularly at borders, may be susceptible to error from normalization and anatomical variability across participants.

Probabilistic atlases would be a better choice (which produce a percentage probability that given coordinates are in a given anatomical region).

in almost all cases, I personally am a strong advocate of checking by visualization. I visually confirm all my coordinate labels and clusters, using both atlas labels and reference to anatomical maps and atlases. Automated systems make mistakes! And anatomical devisions are not as precise as we would like them to be.

On 17 March 2014 13:02, Aser A <[log in to unmask]> wrote:

Hi all,

I have a list of different coordinates ( around 200 ). I also have a brodmann atlas as a nifti file from the software wfu. I would like to find an automated way of labelling these voxels as brodmann areas.

Helps will be appreciated,

Thanks

Aser A