Hi Lisa,
this is a matter often encountered by researchers in neurology so there
are a few ideas. The main issue actually is lesion definition.
In your case, the next steps would seem to be pretty straightforward: as
you have already defined the lesion on the images, you can use these
lesion definitions to mask out the lesions. The key word here is "cost
function masking" for which there are several references in the
literature as well as in the list archives.
Previously, you could supply such a mask during the segmentation
process, but nowadays, you may need to multiply the original image with
the mask such that the lesion is set to 0. This will prevent the most
recent segmentation algorithms within spm to ignore the lesion. You can
use imcalc to this effect (the exact formula would depend on your lesion
masks: if they contain 1's for lesions, you could select the anatomical
and the lesion and try
i1 .* (i2==0)
or so. For the actual segmentation / spatial normalization, you may also
want to check if you still get too much distortion around the lesion
which may be addressed by increasing regularization (see an old paper of
Crinion et al in NeuroImage).
Best,
Marko
Lisa McDermott wrote:
> Hello all,
>
> I have a few subjects with stroke-lesions in their brains. In performing
> normalization, I am afraid that these lesion locations are going to
> disrupt the normalization process. I have drawn lesion ROIs that are in
> the same space as the T1 template. However, I don't know how to use them
> during normalization process. What would be the optimal way to use
> lesion locations during normalization?
>
> This question is probably not just within the confines of SPM. If there
> are other software that I can use, please let me know. Thank you.
>
> Best,
> - Lisa
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
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http://www.medizin.uni-tuebingen.de/kinder/epn/
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