Dear Marko and Christian,
Thanks for the reply. I am following the CAT12 manuscript now to do VBM, Here are some questions I have (with explaining what I did, those part with start are my main questions):
1) CAT12: Segmentation:
a. Volumes: 58 files
b. Options for initial SPM12 preprocessing:
i. TPM: output of TOM8
c. Extended options for CAT12 preprocessing
i. ********Default for all (My concern is about DARTEL and shooting default templates that are based on adults)!! I kept them default as suggested!!
d. Writing options:
i. Grey Matter:
1. Native space: Yes
2. Modulate normalized: Yes
3. DARTEL export: Affine
ii. White Matter:
1. (All options same as above)
2) Run Dartel (create Templates)
a. Images: rp1 affine image
b. Images: rp2 affine image
3) Normalise to MNI Space:
a. Dartel Template: Template-it-6
b. Selecting according to:
i. Flow fields: dependencies (Flow fileds)
ii. Images
1. Images: segmentation; rp1 affine Image
2. Images: segmentation; rp2 affine image
4) Population to ICBM Registration:
a. Dartel Template: Template_it_6
5) Deformations:
a. Composition:
i. Deformation Field: Population to ICBM Registration: Pop2MNI
******As I uploaded attached files, Matlab gave me an error, but still generated 3 folders of labels, mri and report and in mri folder I had all segmentation related files: p1, p2, rp1, rp2, wm, mwp2 and mwp1. No Template was generated!
If you could please help me with this error that would be great.
******let's say I fix this issue after your help. Because I have children dataset, I assume that I should continue with "re-use of customized DARTEL-templates" to do the accurate segmentation. Is that correct or I miss understood? In the documentation in "Segment Data" of this part, mentioned to put wTemplate*_1.nii (which is hopefully the dartel template, first iteration that is generated in last step), what about "shooting template"?
After having Segmentation done again with our customized Dartel Template, I will do smoothing on mwp1 and mwp2 (modulated-normalised to our dartel template-segmented tissues) to use in stats.
Sorry to be so specific. Thanks for you help in advance.
Regards,
Farnoosh
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