In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running?

On Mon, 8 Jul 2013, Jonathan Holt wrote:

As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s <subjID> for the second and third steps of the workflow.

jon

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