Dear SPMers,
I am working with a pediatric population, so I thought it would be a best to create my own template using Template-O-Matic 8. I have done this previously with no luck creating the actual template unless using the scans provided by NIH that uses roughly 400 participants and includes children ages 5-18. This has shown to be beneficial, but because our subject's ages were between 8-12yrs I was hoping to create a template that was more specific to our age groups.
After looking into differences between my settings and the NIH's via print information about TOM.mat, I noticed that NIH consisted of grey matter, white mattter, CSF, BKG1 (background), BKG2, BKG3, and T1 images in contrast to ours which only used GM and WM. I then assumed this must be the reason that I was unable to create a template using our scans. I was unable to obtain any of the BKG files, but knew by running a standard VBM8 estimate and write procedure as described in John Ashburner's manual I would be able to produce these files.
Below I have listed my steps and was wondering if my procedure is correct and if there are any potential errors that could result from using the following procedure:
129 pediatric brain scans were used and consisted of children ages 8-12.
1. run estimate and write using coxxxx files
-Tissue probability Map: TPM.nii
-Affine regularisation: average sized template
Extended options
-spatial normalization: High-dimensional:Dartel
Dartel Template: Template_1_IXI550_MNI152.nii
writing options (used same for GM,WM, and CSF)
-native space:none
-normalized:none
Modulated normalized: non-linear only
DARTEL export: affine
I then left the rest at default
2. estimate regression parameters: selected all GM, WM, CSF, and T1 images that were produced using the VBM8 estimate and write and input them to their appropriate branch.
- input ages and gender in accordance to their input in the previous branches (GM,WM,etc)
3.Create new template: Selected the created TOM.mat file
-selecte template creation method: average approach
- input ages and gender in accordance to their input in the previous branches (GM,WM,etc)
This then gave me 3 files labeled T1_Template_9.545.nii. I apologize for the lengthy post, but I want to be absolutely certain this was performed correctly before I proceed further.
Best,
Jordan Larson
Research Assistant
Department of Psychology
Southern Illinois University - Carbondale
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