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SPM  April 2007

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Subject:

Re: VBM5 problem in young children

From:

Christian Gaser <[log in to unmask]>

Reply-To:

Christian Gaser <[log in to unmask]>

Date:

Wed, 25 Apr 2007 08:32:51 +0100

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Dear Fumiko,

On Wed, 25 Apr 2007 08:45:17 +0200, Marko Wilke <[log in to unmask]> 
wrote:

>Dear All,
>
>> I’m not convinced that this outcome is primarily due to the mismatch 
>> between the characteristics of your study population and the template 
>> (although it might be aggravated by it):
>
>I fully agree. Your imanges look like they were not normalized correctly 
>(remember that even for native-space segmentation, the priors are in 
>efect inversely normalized to the input images). Your results look like 
>they are mainly the result of the prior probability maps. This can 
>happen when matching the priors goes completely wrong which again can 
>happen when you have very inhomogenous input data. This is not 
>high-field data by any chance?
>
>> Is it possible that you didn’t set the origin before preprocessing the 
>> data? In our experience the unified segmentation approach is pretty 
>> vulnerable to end up with such deformed results if you don’t give the 
>> program a reasonable starting point. Assuming that the data quality is 
>> o.k., my best guess would be: reset the origin to AC, rerun data 
>> preprocessing for these subjects, and you’re done.
>
>This may help, too. Christian had implemented an automated determination 
>of the center of mass of an image in order to improve the starting 
>estimates in a beta-version of the 5.1 toolbox but I don't know if it is 
>out yet.

I also assume that spatial registration was not correct. You may try the new VBM5.1 Toolbox, 
which is still a beta version with many new (and not yet documented) features (e.g. correction for 
non-isotropic smoothness, segmentation without priors, pre-registration using center of mass):

http://dbm.neuro.uni-jena.de/vbm/download/

>
>Also,
>
>> The ages of the subjects are 1-3 years old.
>
>there is no reference data for such subjects yet that I am aware of. We 
>(Christian, the Cincinnati IRC group and myself) have two abstracts at 
>HBM where we investigate a prior-less segmentation for datasets from 
>infants. In effect, the segmentation is done as in spm5 but for writing 
>out the results only tissue intensity information is used, disregarding 
>the influence from the priors. It does make the segmentation somewhat 
>more vulnerable, especially w.r.t. inhomogeneity, but it seems to 
>considerably improve segmentation results on "unusual" datasets. Not 
>sure if the updated 5.1 toolbox is already publicly available but you 
>could ask Christian.

Thanks for the push Marko! As he already mentioned, it might be helpful for children/infant data 
to try the new prior-free segmentation approach, which can be found in the extended options.

Best,

Christian

-- 
____________________________________________________________________________

Christian Gaser, Ph.D.
Assistant Professor of Computational Neuroscience
Department of Psychiatry
Friedrich-Schiller-University of Jena
Philosophenweg 3, D-07743 Jena, Germany
Tel: ++49-3641-935805	Fax:   ++49-3641-935280
e-mail: [log in to unmask]
http://dbm.neuro.uni-jena.de


>
>> The segmented images come out like this (please see attached jpg of 
>> brains with modulation, segmentation and normalization applied; the left 
>> brain is the one with the problem, the right brain is for comparison).
>
>Ah, good to know ;) But again, this is a problem with matching the 
>priors and thus effectively a normalization problem. Note the oblique 
>cutoff at the upper left side, this is where either the FOV or the 
>tissue boundary of the input image went. Try the suggestions above and 
>let us know how you fared.
>
>Best,
>Marko
>-- 
>===========================================================
==========
>Marko Wilke                                            (Dr.med./M.D.)
>                 [log in to unmask]
>
>Universitäts-Kinderklinik              University Children's Hospital
>Abt. III (Neuropädiatrie)             Dept. III (Pediatric neurology)
>             Hoppe-Seyler-Str. 1, D - 72076 Tübingen
>Tel.: (+49) 07071 29-83416                   Fax: (+49) 07071 29-5473
>===========================================================
==========
>===========================================================
=============

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