Hello there,
I think that, as he mentioned spatial normalization later-on, there is
no need to reslice at all. Also, I wanted to reiterate (once again ;) my
impression that segmentation profits from a properly-aligned anatomical,
which is easily achieved by coregistering (estimate only) the anatomical
to a T1 template. If one does
coregister only (mean epi to anatomical), take along all functionals
coregister only (anatomical to template), take along all functionals
you moved them twice without reslicing once, which is a bonus. This all
assumes that you realigned (not resliced) them in a first step as
otherwise, the functionals themselves will not be in one space. The
reason for doing it this way is that you now have better starting
estimates for segmentation and you can apply the seg_sn.mat to the
functionals with no worry (if you move either the anatomical or the
functionals after segmentation you have to update the original position
in the seg_sn.mat, which is a bit of a pain and nigh-impossible in new
segment).
Cheers,
Marko
Michael Harms wrote:
> If you've already run the Realignment module and have r* images, those
> are already aligned to the mean EPI, so if you Coregister using the mean
> EPI as the "Reference Image" and SPGR as the "Source Image", there is no
> need to select "Other Images" -- the SPGR will be coregistered into the
> space of the mean EPI, which is the same space that the r* EPI images
> are already in from the realignment step.
>
> cheers,
> -MH
>
>
> functional , On Sat, 2010-12-18 at 16:47 -0500, MCLAREN, Donald wrote:
>> Things that would be better:
>> (1) Use SPM8
>> (2) Switch the reference and source images and then you don't need to
>> select any images
>>
>>
>> The T1 will then be in line with the EPI.
>>
>> Best Regards, Donald McLaren
>> =================
>> D.G. McLaren, Ph.D.
>> Postdoctoral Research Fellow, GRECC, Bedford VA
>> Research Fellow, Department of Neurology, Massachusetts General
>> Hospital and Harvard Medical School
>> Office: (773) 406-2464
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>>
>> On Sat, Dec 18, 2010 at 4:37 PM, John Gelburg<[log in to unmask]>
>> wrote:
>> Hi,
>>
>>
>> Currently I am doing the SPGR-EPI co-registration in the
>> following way and I see that the images do not exactly match.
>> 1. Coreg: Estimate option
>> 2a. Reference Image: mean image from realignment step
>> 2b. Source Image: SPGR image
>> 2c. Other images: all the EPI images
>>
>> In the subsequent steps I segment the co-registred SPGR image
>> and then use the *_sn.mat for normalization.
>> What can I do better? It's desirable to be able to run the
>> whole process automatically.
>>
>> Thanks,
>> John
>>
>>
>>
>>
>>
>>
>
--
____________________________________________________
PD Dr. med. Marko Wilke
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Marko Wilke, MD, PhD
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