Dear John, Elliott,


Thanks. Just a comment on two of the points made  - 

1. I don't think the AAL mask is trying to be "too precise", rather the contrary: I've just measured the AAL hippocampi and they weigh in at a hefty ~7,500mm^3. Ok, they're in Colin Holmes / MNI space which is about 35% (Ashburner et al. 1997) to 46% (Hammers, Allom et al. 2003) bigger than average, but still they're big - as partly explained by the protocol (Tzourio-Mazoyer et al. 2002). For comparison, our protocol (Niemann K et al. 2000) yields volumes of about 2100mm^3 in native space and 3300mm^3 in MNI space (Hammers, Allom et al. 2003); they are the volumes that went into the maxprobmap in MNI space recently discussed here. There are reviews/overviews of protocols and differences (e.g. Konrad C et al. 2009).

If a "GM only" mask bothers you, you can always get rid of the "holes" with simple morphological operations - e.g. by smoothing say with a 4mm kernel and then thresholding back. Obviously if you loose many voxels, your activation may not be in the hippocampus at all - which might also be interesting.


2. "moreover, it's not left-right symmetric": Well, why would it be? The physiological R>L asymmetry is well known (e.g. Pedraza O et al. 2004), certainly depends a bit on protocols, but should probably be around 5-12%; personally I use its detection as a rough indicator of the quality/plausability of a delineation protocol. In the case of AAL, it's present but a bit small at 1.5% (remember this is an atlas based on a _single_subject_). Ignoring the physiological asymmetry is in my view dangerous, especially when clinical decisions are at stake, as for example in epilepsy surgery (see Hammers et al. NI 2007 for a discussion with example).
The only instance when hippocampi would be expected to be symmetrical is when only _one_hemisphere_ is available and then mirrored, as in the Talairach atlas (and derivatives). But of course that carries no information about physiological asymmetry.

Hope this helps,

Best wishes,

Alexander





-----------------------------
Alexander Hammers, MD PhD





Chair in Functional Neuroimaging
Neurodis Foundation
http://www.fondation-neurodis.org/
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CERMEP – Imagerie du Vivant
Hôpital Neurologique Pierre Wertheimer
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Other affiliations:

Visiting Reader; Honorary Consultant Neurologist
Division of Neuroscience and Mental Health, Faculty of Medicine
Imperial College London, UK
---------------------------------
Honorary Reader in Neurology; Honorary Consultant Neurologist
Department of Clinical and Experimental Epilepsy
National Hospital for Neurology and Neurosurgery/ Institute of Neurology, University College London, UK




On 21 Feb 2011, at 13:50, John Fredy wrote:

Thanks Alexander, Michael and Elliot for the reply, I will see the AAL atlas and the  maxprobmap more deeply. I am in the beggining in fmri in the hippocampus for 
epilepsy patients, so, I will have time to explore more and more in working with roi analysis.

Best wishes from Antioquia

On Sun, Feb 20, 2011 at 10:35 PM, G Elliott Wimmer <[log in to unmask]> wrote:
Hi,

Regarding the AAL template (which is most likely what you have already seen in the WFU pickatlas), I too have noticed that the AAL hippocampus definition tries to only cover grey matter. This exclusion leads to gaps and holes in the mask that I think you are referring to.

Given the anatomical variability between subjects in the hippocampus, it appears to me that the AAL mask attempts to be far too precise; moreover, it is not left-right symmetric.  In the past, I have used AFNI's 'draw dataset' function to correct these problems with the AAL mask and used the resulting modified mask to define ROIs.

Alternatively, I've seen probabilistic anatomical masks that I think were used in FSL, and that may be worth checking out.

Best Regards,

G Elliott Wimmer

Dept. of Psychology
Columbia University