Hi,

due to Friday afternoon and the current heatwave, I will only answer in
very general terms:

- I cannot judge whether using your own DARTEL template is a good idea
as I do not know how large your group is (my hunch is it should be
really large for this to be a good idea)

- I am not a believer that a given space (in this case, MNI) is
automatically better than another; if you use custom templates, I find
it equally legitimate to describe your results based on where they are
in your template

- finally (pardon my bluntness), lack of familiarity with a given
approach is not a strong scientific argument (it also hurts my pride as
I invested several hours into writing a manual for COM)

Hope this helps
Marko

Ariadna Albajara Sáenz schrieb:
>
> Dear Marko and Helmut,
>
> Thank you for the feedback. I wanted to check if the steps I followed
> are correct in case these could explain my results.
> After checking data quality and excluding participants with
> artefacts/motion, I followed the following steps (taking into account
> that I have a pediatric sample aged 8-12 and that I am using TOM8 and
> DARTEL since I am more familiar with these than Cerebromatic):
>
> 1. I created customized TPMs using TOM8.
>
> 2. Then I created a DARTEL template using segmentation (grey matter
> ->Dartel export affine, white matter -> Dartel export affine) and here I
> entered already the previously created TOM8 TPMs.
>
> 3. Then I used "DARTEL tools--> normalise to MNI space" (I did this
> because it is in the Manuel although this creates a ".mat" file called
> "Template_6_2mni.mat" and  the images "smwrp1_XXXX-affine.nii" and
> "smwrp2_XXXX-affine.nii", which I do not use in the following steps SO I
> DON'T KNOW IF THIS STEP IS NECESSARY?).
>
> 4. Then I did "DARTEL ICBM --> population to ICBM registration" where I
> entered the file "Template_6" created in the step 2.
>
> 5. After this, I did "SPM-> Util--> deformations" where I entered the
> "y_Template-6-2mni.nii" file created in the step 4 and under "Apply to"
> I entered the Templates 0 to 6 created in step 2. This creates the files
> wTemplates 0 to 6
>
> Finally I do segmentation entering the ORIGINAL T1 images but this time
> entering the TPMs created with TOM8 in "Tissue Probability Map" and the
> file "wTemplate_1.nii" in Dartel template. Is this correct? is it
> correct to enter the original T1 images here?
>
>
> Does this seem correct?
>
> I was also wondering if the subsequent statical maps would be in MNI
> space or not.
>
> Thanks a lot for your help.
>
> *Ariadna Albajara Sáenz*
> _[log in to unmask] <mailto:[log in to unmask]>_
> UR2NF - Neuropsychology and Functional Imaging Research Group
> CRCN - Center for Research in Cognition and Neurosciences
> http://crcn.ulb.ac.be/
> *
> *
> UNIVERSITÉ LIBRE DE BRUXELLES, Avenue F. Roosevelt 50, CP 151, 1050
> Brussels (Belgium).
> Office: DB10-237
>
>
> El jue., 25 jul. 2019 a las 12:54, MRI More (<[log in to unmask]
> <mailto:[log in to unmask]>>) escribió:
>
>     Dear Ariadna,
>
>     The glassbrain image looks a bit noisy, which doesn't have to mean
>     anything though. Based on the location, the MRI image seems to
>     indicate GM differences in the caudate nucleus and the basal ganglia
>     more generally. Please note that parts of the basal ganglia and the
>     thalamus are quite difficult to identify in certain templates due to
>     poor GM-WM contrast.
>
>     Did you use the Dartel or Shoot template as included in CAT12 for
>     the high-dimensional registration part? In that case, it might be
>     wise to overlay the results onto the corresponding template (GM-WM
>     contrast for basal ganglia should be better), or even better, create
>     a mean image of the normalised (bias corrected) structural volumes
>     of your study, or alternatively, of the normalised modulated or
>     unmodulated GM files as obtained from CAT12 preprocessing. IMO it's
>     always preferable to map results on some image derived from your own
>     data. If there were some issues during the
>     segmentation-normalisation, resulting in enlarged ventricles
>     relative to the templates / priors, it would obviously be misleading
>     to rely on a mapping onto those templates.
>
>     Best regards
>
>     Helmut
>

--
____________________________________________________
Prof. Dr. med. Marko Wilke
  Facharzt für Kinder- & Jugendmedizin, Neuropädiater
  Leiter, Experimentelle Pädiatrische Neurobildgebung
  Geschäftsführender Oberarzt der Abt. Neuropädiatrie
  Universitäts-Kinderklinik

Marko Wilke, MD, PhD
  Pediatrician and Pediatric Neurologist
  Head, Experimental Pediatric Neuroimaging
  Senior Consultant in Pediatric Neurology
  University Children's Hospital

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/
____________________________________________________