Hi Tracy,
my best guess would be that the segmentation routine gets hung up on
your image inhomogeneities, of which there seems to be quite a bit (note
how the anterior part of the brain is already visibly much brighter). If
you wanted to go with segmenting/normalizing your EPIs directly, I have
suggested using a two-pass procedure in the past (run segmentation once
on the mean EPI and only write out a bias-corrected image in native
space, on which you then run segmentation again to achieve
normalization), and only very few people complained to me afterwards :)
This may also need some playing with the bias field options.
Cheers,
Marko
Luks, Tracy wrote:
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> I'm having trouble with the normalization of some 3T epi images acquired with a 32 channel head coil. The normalization of the EPI images to the EPI template runs properly, but the resulting images are clearly not matching the template, particularly in the posterior brain. I haven't had problems like this with images acquired on different scanners. I have also tried coregistering the EPI images to the T1, normalizing the T1, and applying those parameters to the EPIs. That is more successful, but I'd still like to know what's going wrong with the EPI to EPI normalization, and what I can do to rectify the problems. The attached images show the "check reg" results with the "normalized" EPI and the template EPI images.
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> Thanks
> Tracy Luks
> UCSF
> [cid:f7a170cf-4ba5-46df-b68a-13725679a7b8@ucsf.edu]
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--
____________________________________________________
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
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn
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