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SPM  December 2010

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Subject:

Re: co-registration in SPM5: how to make best of it?

From:

Marko Wilke <[log in to unmask]>

Reply-To:

Marko Wilke <[log in to unmask]>

Date:

Tue, 21 Dec 2010 08:34:58 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (119 lines)

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
>> =====================
>> This e-mail contains CONFIDENTIAL INFORMATION which may contain
>> PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED
>> and which is intended only for the use of the individual or entity
>> named above. If the reader of the e-mail is not the intended recipient
>> or the employee or agent responsible for delivering it to the intended
>> recipient, you are hereby notified that you are in possession of
>> confidential and privileged information. Any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the
>> contents of this information is strictly prohibited and may be
>> unlawful. If you have received this e-mail unintentionally, please
>> immediately notify the sender via telephone at (773) 406-2464 or
>> email.
>>
>>
>> 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
  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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