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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] <[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]>) 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]>_ > > 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/ > ____________________________________________________ > >