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]
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
|