Hi
Many thanks. All the comments are very helpful. I managed to get a better normalisation after I delete all the files and convert the data and do the whole thing again.
Best wishes
Nichol
________________________________________
From: Marko Wilke [[log in to unmask]]
Sent: 26 February 2013 17:15
To: mlnwong; [log in to unmask]
Subject: Re: [SPM] Normalisation problem
Hi,
what you need to watch out for is that manual reorientation should not
occur after coregistration, or that it should then be applied to both
datasets in the same way. Ultimately, (1) the images should be nicely
aligned with the priors before segmentation and (2) they need to be in
register if parameters from processing one modality are to be applied to
another modality. (1) you can achieve by manual reorientation, and (2)
you can achieve by coregistration. If you do 1, 2, that's fine, if you
do 2, 1, you're likely to run into problems (if you only reorient one
modality, or independently reorient the other modality).
Cheers,
Marko
mlnwong wrote:
> Hi
>
> Thanks for your advices. What if the reorientation is applied to both anatomical and functional data like it suggested 'interactively'? Will this still be a problem?
>
> Best wishes
> Nichol
> ________________________________________
> From: Marko Wilke [[log in to unmask]]
> Sent: 26 February 2013 16:58
> To: mlnwong; [log in to unmask]
> Subject: Re: [SPM] Normalisation problem
>
> Hi,
>
> two remarks on your pipeline: one, if you manually reorient after
> coregistration (not sure if you did), this may be a problem if you
> segmented the anatomical and applied the parameters to the functional
> (not sure if you did that either), as the images will not be in register
> anymore.
>
> Cheers,
> Marko
>
> mlnwong wrote:
>> Hi
>>
>> I have used the DPARSFA to do the 'Remove first 10 time points', 'Slice timing', 'Realign', 'Reorient after Coreg Interactively', & 'Segment' before normalisation.
>>
>> Thanks
>> Nichol
>> ________________________________________
>> From: Will Moore [[log in to unmask]]
>> Sent: 26 February 2013 16:18
>> To: mlnwong
>> Subject: Re: [SPM] Normalisation problem
>>
>> Sorry that wasn't helpful. What steps did you use for preprocessing? It would be easier to know what to suggest if we know how you processed your images.
>>
>> ~Will
>>
>> On Feb 26, 2013, at 12:15 AM, mlnwong <[log in to unmask]> wrote:
>>
>>> Thanks Will. I have tried this before but it doesn't help much.
>>>
>>> Best
>>> Nichol
>>> ________________________________________
>>> From: Will Moore [[log in to unmask]]
>>> Sent: 26 February 2013 16:12
>>> To: mlnwong
>>> Cc: [log in to unmask]
>>> Subject: Re: [SPM] Normalisation problem
>>>
>>> You might try manually setting the origin using spm's Display function. Manually correcting what appear to be relatively severe rotations in all three planes could significantly enhance the quality of normalization.
>>>
>>> ~Will
>>>
>>> On Feb 25, 2013, at 11:08 PM, mlnwong <[log in to unmask]> wrote:
>>>
>>>> Hi all
>>>>
>>>> It appears that the normalisation has failed in this subject because of the poor functional data acquired. Any advice?
>>>>
>>>> Thanks.
>>>>
>>>> Best wishes
>>>> Nichol
>>>> <functional.png><functional_axial.png><normalisation.PNG>
>>>
>>
>
> --
> ____________________________________________________
> 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/
> ____________________________________________________
>
--
____________________________________________________
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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