On 3 Jul 2008, at 15:10, Markus Gschwind wrote:
Hi Saad!
1) the first one should work. what happens when you do that?
In fact there were two problems.
1. Problem of loop in my script ;-/
that's good news for proj_thesh!
2. It seems like the file "total.nii.gz" is only created if I go directly into the directory to run the proj_thresh
cd ${groupprobtrackxdir}/rawseeds/${myside}${myseed}/
proj_thresh *seed.nii.gz 10
but NOT if I do it like this, using the whole filename:
proj_thresh ${groupprobtrackxdir}/rawseeds/${myside}${myseed}/*seed.nii.gz 10
How come?
... and that's proj_thesh's fault:)
the file total.nii.gz will be created in the directory from which you run the command... a quick fix is to log into the probtrackx directory before running proj_thesh..
note that you don't really need total.nii.gz, since it is already used internally by proj_thesh
Saad.
Tanks!
Markus
