Hi Scott,

You can do trac-all -prep first, to make sure you generate all the files needed for path reconstruction (including generating priors and masks from freesurfer recons), then move all your bedpostx files to the dmri.bedpostX as Anastasia mentioned and then do trac-all -path (for tract reconstruction). That should typically work.

-Priti

Hi Scott - The bedpost outputs are expected to in a directory called dmri.bedpostX under the subject's trac-all output directory. You can put all your bedpost outputs there and proceed at your own risk!

There's a description of other trac-all outputs from the steps before bedpost here: http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#OutputDirectoriesandFiles

The bedpost step in trac-all would normally use eddy_corrected data and and an anatomical brain mask from the FS recon, but otherwise there shouldn't be other dependencies on previous steps.

Hope this helps, a.y

On Wed, 15 Jun 2011, Scott Sorg wrote:

...

Hello,

If I already ran bedpostx on my diffusion data, how can I skip this step in tracula and still get it to run smoothly.

Thank you,

Scott

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