I see now. If the orientation information is incorrect, this will continue
to be a problem. It sounds like you have access to the dicoms? If so, it's
better to wait and use those.
Allison
On Mon, 8 Jul 2013, Jonathan Holt wrote:
Allison I'm running the following
recon-all -all -s <subjID> -i path/to/nifti
attatched is the error recon log
I've already gone over this with bruce, martin. It seems as if the 001.mgz,
orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming
straight out of the nifti files I've passed and these mgz's are generated
before the recon-all process exits with errors.
On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote:
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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