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Thanks John... Date: Thu, 16 May 2013 14:28:55 +0000 From: [log in to unmask] Subject: Re: [FSL] How to buid a MRI template image without a reference in FSL? To: [log in to unmask] See Sanchez et al (2011) and 2012. Sanchez, C.E., Richards, J.E., & Almli, C.R. (2012). Age-specific MRI brain templates for pediatric neuroimaging. Developmental Neuropsychology, 37, 379-399.(pdf ) Sanchez, C.E., Richards, J.E., & Almli, C.R. (2011). Neurodevelopmental MRI brain templates for children from 2 weeks to 4 years of age. Developmental Psychobiology. Doi:10. 1-02/dev20579; 57, 77-91.(pdf ) 1—Register your heads or brains to a brain that is even remotely similar; use flirt with –dof 6, this will do a rigid rotation and translation. So the brain (or head) will not be warped or sized. Do an average based on this, this is T0 2—Register the heads to this T0, with rough resolution and increasing resolution (maybe flirt. The first average (T1) will be the goat brains registered to the very rough T0 average brain, all made of goats. The main reason for step1 is to get all the original brains roughly positioned in space (rotate, translate) and the subsequent steps are to transform the brains before averaging (e.g., flirt , fnirt, ANTS). John *********************************************** John E. Richards Carolina Distinguished Professor Department of Psychology University of South Carolina Columbia, SC 29208 Dept Phone: 803 777 2079 Fax: 803 777 9558 Email: [log in to unmask] HTTP: jerlab.psych.sc.edu ************************************************* From: Von Click <[log in to unmask]> Reply-To: FSL Library <[log in to unmask]> Date: Thursday, May 16, 2013 5:03 AM To: FSL Library <[log in to unmask]> Subject: [FSL] How to buid a MRI template image without a reference in FSL? Hi everyone! I would like to build a template image from MRI images of goat brains with FSL. My problem is that it does not yet exist a MRI brain atlas of this species. Therefore, I do not have a reference image on which I can register all my images in order to compute an average image which I will use as a template 0 at the next iteration. Does anyone have an idea of how to proceed? Thank you in advance. Best regards. Arsene