Hi Jale,
I think it is difficult to give a general one-size-fits-all answer for
this. From what you write, you may have two issues in your data, one
being inhomogeneity (high-field scanner? multi-channel headcoil? imaging
sequence?), the other being a limited field of view (pulling data from
native space to regions in normalized space that were not imaged). You
would have to do different things to address these.
For the former, I still like my original suggestion, but playing around
with the bias estimation parameters may be required (in order to then
visualize your bias field, subtract the bias-corrected from the original
image). Usually, inhomogeneities should be less pronounced in
anatomicals, so I do not know why this did not work for you (unless, as
John keeps pointing out, if the images are not well-aligned due to the
inhomogeneities, then applying parameters from the one to the other will
not work).
For the latter, an explicit mask during estimation of the spatial
normalization parameters may help (or less non-linear deformation). But
of course, if the simplest approach (segmenting the mean EPI) works best
for you, who am I to not do it ;)
Cheers,
Marko
Jale Özyurt wrote:
> Dear Dr. Wilke,
>
> I have a similar problem with inhomogeneities in my EPI images. I have
> tried the two pass procedure as suggested below
> ( 1. running segmentation on the mean EPI, 2. running segmentation on
> the bias corrected mean obtained by this procedure and normalizing the
> EPIs by using this mmean*seg_sn.mat)
> I found that the normalized EPIs also covered brain regions that were
> not imaged (lower part of the temporal lobe, cerebelllum).
>
> I have also tried to segment the bias corrected anatomical image to get
> better normalization parameters for the EPIs, which was not satisfactory.
>
> When I use mean*seg_sn.mat that was obtained by the EPI segmentation
> (not bias corrected, I guess) , I get reasonable results.
>
> I wonder, whether it is allowed to do so.
>
> Thank you very much in advance.
> Kind regards
> Jale Özyurt
>
>
> Am 28.03.2012 08:31, schrieb Marko Wilke:
>> 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:
>>>
>>>
>>> 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.
>>>
>>> Thanks
>>> Tracy Luks
>>> UCSF
>>> [cid:f7a170cf-4ba5-46df-b68a-13725679a7b8@ucsf.edu]
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
--
____________________________________________________
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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