Sarah,
> Thank you for your response. I'm going to play around with the affine
> transformation---good call.
Good luck :)
> I'm also noticing a difference when I use to different processing streams:
> 1) New Segment --Dartel ---Normalise
> versus
> 2) VBM8 --smooth
They are using different methods for segmentation and normalization, so
the fact that you find differences is not surprising in and of itself
(actually, I think Christian Gaser would rightfully be very disappointed
if you would not find differences as he put a lot of work into vbm8 :)
Now, the real question is, which one is closer to the ground truth,
which will be a much harder one to answer.
> I'm not sure why I'm getting the difference---having no problems using
> the VBM toolbox, so perhaps I'll stick with that.
Practicality of course is one important aspect, but there may be more
tangible arguments, such as using a priorless segmentation when dealing
with unusual populations, that you may want to look into before making
that decision.
Cheers,
Marko
> On Fri, Mar 13, 2015 at 3:10 AM, Marko Wilke
> <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi Sarah,
>
> Attached I have one final smoothed segmentation of a subject,
> from my
> child patient sample, that looks bizarre. I have 6 other brains that
> look similar, all from the patient group. None of the other brains,
> patient or control, look this way (e.g. shifted far left, rotated,
> etc). All structurals were manually realigned, all processed
> together
> (maybe this is the problem?), using new segment, then Dartel, then
> normalize, smooth
>
>
> Such overt failure usually is caused by the affine transformation
> going wrong, which again is caused by (usually) strong image
> inhomogeneities or unusual brains (more likely in your case).
> Depending on how young the subjects are, you may want to play with
> the regularization of the affine transformation. To narrow it down,
> it would be important for you to find out when things went astray (I
> would guess right after new segment but better check).
> Alternatively, might you have reoriented the data accidentally?
>
> 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
> Fax +49 7071 29-5473
> [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/
____________________________________________________
|