 |
 |
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/ ____________________________________________________