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Thanks Marko!

Just to be follow up for clarity: when running DARTEL create template for
each patient together with all 70 controls (70c+1p), I will have to do this
for each patient separately, right? When for example one day by chance I
have several (np) patients, it will not be possible to run them together
(70c+np), but I need to run it each time again n * (70c+1p), right?

Using the SPM template or the IXI created template is equally unfair for
all, true, but it actually means the systematic bias is just let in the
dark and I have no guarantee that it is not affecting the results. I even
don't know form which scanner, population etc. those templates are created,
compared to the one created by my controls which correspond to the same
scanner, the same age and sex of my patients... So I am not sure what is
better!

Best,
Markus


2014-04-07 9:39 GMT+02:00 Marko Wilke <[log in to unmask]>:

> Hi,
>
> > Good point. Anyway, creating new DARTEL templates does not take too much
> > time, I saw.
>
> Well, you can see if this is the way you want to go. But then again, you
> could also use an externally-generated DARTEL template (such as the one
> coming with vbm8), or you could generate one from a control population
> that neither the patient nor your controls contributed to (such as the
> IXI dataset). This would then be "equally unfair" to both.
>
> > Sorry to insist, but what about my second question:
> >
> >     Is there a recommended way how to normalize the whole T1 image? Is
> >     it automatically done when I select the initial T1 together with the
> >     c1, c2, c3 images in the normalizeMNI step? I am not sure if the
> >     image look OK like this.
>
> I do not use DARTEL much, and if so, from the command line, and not for
> the T1. Have you tried it to see what it looks like? What does the
> manual say? Can you take the deformation fields and apply them?
>
> Cheers,
> Marko
>
> > 2014-04-07 8:50 GMT+02:00 Marko Wilke <[log in to unmask]
> > <mailto:[log in to unmask]>>:
> >
> >     Hi Markus,
> >
> >      > Thanks for your diverse input ;-)
> >
> >     That's science :)
> >
> >      > @Marko: Yes, I plan to compare each patient to the healthy data
> >     base of
> >      > 70 patients (detection of local pathology).
> >     [...]
> >      > So is the difference of 1 additional patient in the 70 other
> subjects
> >      > really critical, given the smoothing, the SNR etc.?? Has this been
> >      > evaluated?
> >
> >     Not sure this has been evaluated rigorously, but my usual point is:
> what
> >     do you reply to a reviewer who asks you to demonstrate why the
> >     difference between subjects that you see in the end is not due to a
> >     difference in data processing? And your answer is going to be "I
> hope it
> >     is not" because you cannot prove it. If you have processed your
> controls
> >     in a systematically different way than your patient, this is simply
> an
> >     irreconcilable difference that you cannot make up. It is like
> scanning
> >     children on one scanner and adults on another scanner and then
> finding
> >     the effects of age. You cannot, as age is confounded by scanner
> >     difference. In how far this effect is huge, I cannot tell you, but
> then
> >     again, you do not usually look for huge effects in a patient anyway.
> >
> >     Cheers,
> >     Marko
> >     --
> >     ____________________________________________________
> >     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/
> >     ____________________________________________________
> >
> >
>
> --
> ____________________________________________________
> 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/
> ____________________________________________________
>
>