FYI, this is what I finally did to create the skeleton (it could be of help to another newbie like me :), being all_FA the 4D volume with all the FA images already registered, and 300 my FA threshold based on visual inspection (FA ranging from 0 to 1000 in my particular case):
Thanks David. I will play around with the script and see what happens.Best,MiguelOn Tue, Feb 16, 2010 at 5:47 PM, David Flitney <[log in to unmask]> wrote:
I suspect not. Despite it's name, the tbss_3_postreg script, is actually doing registration stages. Instead, if you take a look at the script then I think you need to manually run stages after/around that with the line:echo "merging all upsampled FA images into single 4D image"Note the call to tbss_skeleton.Hope that helps.On 16 Feb 2010, at 16:22, Miguel Burgaleta wrote:Hi FSL experts,I need to combine an in-house image registration protocol with TBSS. I was wondering if it is possible to feed tbss_3_postreg with a 4D file made of images that are already nonlinearly registered. I would just need to create the mean of those FAs and make the skeleton from it, right? I believe the former step can be easily given with fslmaths, but I don't see a straightforward way to make the skeleton with FSL's tools. Any help will be highly appreciated.Thanks in advance,Miguel--Dave Flitney, IT ManagerOxford Centre for Functional MRI of the BrainE:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717