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SPM  December 2013

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Subject:

Re: Activation outside glass brain

From:

Marko Wilke <[log in to unmask]>

Reply-To:

Marko Wilke <[log in to unmask]>

Date:

Wed, 18 Dec 2013 08:09:37 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (207 lines)

Andy,

for normalization to go wrong as in your example, there (still) are two 
main candidates: one, the normalization itself failed (as suggested by 
John, and thus a priori far more likely :). To test this, you must look 
at the output of the normalization process, e.g., look at the normalized 
T1 if you used unified segmentation. Two, the images you applied the 
normalization parameters to were not in register with the image you 
normalized. To ensure this, one uses coregistration. This involves 
matching the (e.g.) mean epi to the anatomical AND taking along all the 
other functionals by selecting them in the "other images" option. If you 
only coregistered the mean epi, this would explain your problems.

Good luck,
Marko

Andy Yeung wrote:
> Dear all,
>
> I have gone back to re-do everything.
> Check Reg after realignment (Est&Res) shows mean EPI is not aligned with
> spm8 templates (T1 template) while other subjects more or less do.
> If I rotate and align manually mean EPI with structural or T1 template,
> other hundreds of EPI data won't follow, so what should I do?
> I sincerely thank everyone for your patience.
>
> Yours faithfully,
> Andy
>
>
> On Wed, Dec 18, 2013 at 9:04 AM, Andy Yeung <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
>     Dear Lei Gao,
>
>     What images should I reorientate to AC before normalization?
>     rs file of structural.
>     How about rs of EPI data? There're so many files of rs of EPI.
>
>     Yours sincerely,
>     Andy
>
>
>     On Wed, Dec 18, 2013 at 8:50 AM, Lei Gao <[log in to unmask]
>     <mailto:[log in to unmask]>> wrote:
>
>
>         reorientation to AC before normalization
>
>
>
>
>
>         At 2013-12-18 08:16:43,"Andy Yeung" <[log in to unmask]
>         <mailto:[log in to unmask]>> wrote:
>
>             Dear all,
>
>             Attached window shows mean, rs and wrs accordingly.
>             So is it that segmentation and normalization both wrong?
>             Sorry I don't know how to rectify as I skimmed through the
>             mailing list by typing wrong normalization...
>
>             Yours faithfully,
>             Andy
>
>
>             On Tue, Dec 17, 2013 at 9:51 PM, Marko Wilke
>             <[log in to unmask]
>             <mailto:[log in to unmask]>> wrote:
>
>                 Andy,
>
>                 as John mentioned yesterday, this very likely is a case
>                 of the affine part of spatial normalization gone bad.
>                 You can check that by looking at the normalized image,
>                 which is much more sensitive than looking at the glass
>                 brain. Once you found the step where things have gone
>                 wrong, search the list archives
>                 (www.jiscmail.ac.uk/cgi-bin/__webadmin?S1=spm
>                 <http://www.jiscmail.ac.uk/cgi-bin/webadmin?S1=spm>) for
>                 ideas as to reasons and solutions.
>
>
>                 Good luck,
>                 Marko
>
>                 Andy Yeung wrote:
>
>                     Dear all,
>
>                     I used Display button to manually rotate mean
>                     functional image and
>                     structural image, then Check Reg to confirm visually
>                     that they were
>                     quite well aligned to each other.
>
>                     Then I performed coregistration, segmentation,
>                     normalization, smoothing
>                     and specification as for other normal subjects' data.
>
>                     Attached is the results window. Now the wms looks
>                     quite beautiful and
>                     normal, but the activation shifts anteriorly. And
>                     it's still outside the
>                     glass brain.
>
>                     Sorry for your time, could anyone help?
>                     Thanks a lot.
>
>                     Best,
>                     Andy
>
>
>                     On Tue, Dec 17, 2013 at 6:46 AM, Colin Hawco
>                     <[log in to unmask] <mailto:[log in to unmask]>
>                     <mailto:[log in to unmask]
>                     <mailto:[log in to unmask]>>__> wrote:
>
>                          Did you check your
>                     registrations/normalizations? This looks like the
>                          problem to me, at a glance.
>
>
>                          On 16 December 2013 03:20, Andy Yeung
>                     <[log in to unmask] <mailto:[log in to unmask]>
>                          <mailto:[log in to unmask]
>                     <mailto:[log in to unmask]>__>> wrote:
>
>                              Dear all,
>
>                              I have finished data input for 13 subjects,
>                     all were fine.
>                              But the 14th subject got the activation
>                     like this: outside the
>                              glass brain.
>                              I repeated standard procedures from
>                     realignment, coreg, segment,
>                              normalize, smooth.
>
>                              Could anyone suggest what was going wrong?
>                              Thanks a lot.
>
>                              Yours faithfully,
>                              Andy
>
>
>
>
>                 --
>                 ______________________________________________________
>                 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 <tel:%2B49%207071%2029-83416>
>                   Fax +49 7071 29-5473 <tel:%2B49%207071%2029-5473>
>                 [log in to unmask]
>                 <mailto:[log in to unmask]>
>
>                 http://www.medizin.uni-__tuebingen.de/kinder/epn/
>                 <http://www.medizin.uni-tuebingen.de/kinder/epn/>
>                 ______________________________________________________
>
>
>
>
>
>

-- 
____________________________________________________
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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