Thank you very much for your answer, I will check that out :)
*Ariadna Albajara Sáenz*
*[log in to unmask] <[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 lun., 29 jul. 2019 a las 11:40, Marko Wilke (<
[log in to unmask]>) escribió:
> Hello,
>
> with regard to the first part, is using a custom template in children
> aged 8-12 a good idea, my reply would be "definitely".
>
> With regard to the second question ("how many subjects do I need for my
> own templates"), I refer to Figures 6 & 7 in the paper at
> https://doi.org/10.3389/fncom.2017.00005 The simulations therein (to me)
> conclusively demonstrate that there is a substantial difference between
> priors generated from 25, 50, or 100 subjects, and a gold standard, and
> that this difference is substantially lower for com-priors.
>
> Cheers
> Marko
>
> Ariadna Albajara Sáenz schrieb:
> > Dear Marko,
> >
> > Thank you for your answer. My sample has 73 children (56 after excluding
> > the children with motion). Do you think in this case it is appropriate
> > to use a customized DARTEL template ?and customized TPMs?
> >
> > You are right, I will check out Cerebromatic! ;)
> >
> > Thanks again,
> >
> > *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 vie., 26 jul. 2019 a las 15:47, Marko Wilke
> > (<[log in to unmask]
> > <mailto:[log in to unmask]>>) escribió:
> >
> > 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]>
> > <mailto:[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]>
> > > <mailto:[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]
> > <mailto:[log in to unmask]>
> >
> > http://www.medizin.uni-tuebingen.de/kinder/epn/
> > ____________________________________________________
> >
>
> --
> ____________________________________________________
> 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/
> ____________________________________________________
>
>
