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Subject:

Re: cerebr-o-matic toolbox and CAT12

From:

Marko Wilke <[log in to unmask]>

Reply-To:

Marko Wilke <[log in to unmask]>

Date:

Mon, 2 Oct 2017 18:48:29 +0200

Content-Type:

text/plain

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text/plain (74 lines)

Hello Alain,

I would think there may be two problems here, but both seem to be due to 
using customized priors. The first issue you observe may or may not be 
relevant, which is hard to say as you do not state whether you obtain 
any output files at all. If the outputs look ok, then the warning 
message (#1) may or may not be relevant. If processing aborts, then this 
sounds more serious, but in this case I would divert to Christian as it 
is his warning ;)

In the second case, the last volume should indeed not be all zeros. When 
generating your own regression parameters, did you provide 6 tissue 
class images per subject? And do the first 5 volumes of the TPM you 
create sum to 1? And are the doscale and the add2last flag in mw_com_gen 
set to 1, and what happens if you set either to 0 instead?

Cheers
Marko

Alain Imaging schrieb:
> Hi everybody (and I guess Marko Wilke and Christian Gaser if you're reading this) !
>
> I have been trying to use the cerebr-o-matic toolbox to obtain tailored TPM for my developmental sample to use to perform segmentation with the CAT12 toolbox.
>
> Some words on my sample: I have 100 children between 8 and 12.5 years. They belong to three groups: typically developing children; dyslexic and ADHD. I want to compare these groups in terms of different brain characteristics, including cortical thickness and GMV in a specific set of regions.
>
> I decided to take some time to find out what it can be the best approach to segment and obtain cortical thickness and GMV for this sample. To this end I wanted to compare the final results (i.e. segmented images) using (1)SPM12 with the standard prior, (2)using prior from the COM toolbox using the provided parameters and (3)using prior created estimating my own sample parameters (including in the model age, sex and diagnosis).
> The process of creating the prior with the COM toolboxes worked fine: both using the parameters provided with the toolbox and estimating my own sample parameter led to the creation of a 6D volumes that look fine (except for the fact that the 6th volume - that if I got it correctly model the background - of each 6D volume has zero everywhere).
>
> However, when I try to use these priors with CAT12, I got two different error messages:
> -when using the prior calculated using the provided parameters I got an error saying :
>     "WARNING: Inverse tissue contrast!
>     (BG=5.40, CSF=1360.58, GM=578.46, WM=159.68)
>     AMAP estimated untypical tissue peaks that point to an
>     error in the preprocessing bevor the AMAP segmentation."
> -when using the in-sample parameters I got an error saying:
>     "No largest WM cluster could be found:
>     Please try to set origin (AC) and run preprocessing again
>     because it is very likeli that spatial normalization failed."
>
> Note that when I try to process the same T1 images using the standard SPM12 prior everything run pretty smooth.
>
> Do you have any idea about what is going wrong ? Is there something obvious that I am missing ? Is the culprit the fact that the background prior is uniform (=0) the culprit ? And is there a way I can fix this in the COM pipeline ?
>
> Thanks in advance for any help you can provide
>
> Best
>
> Alain
>

-- 
____________________________________________________
Prof. 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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