As you have discovered, when using mgz format, the orig.mgz should be
in the mri dir. If you have multiple runs, then they should go under
mri/orig/001.mgz ...
don't know about the seg fault.
doug
David Soscia wrote:
Thanks, after a little tweaking, I managed to get part of the process
Thanks, after a little tweaking, I managed to get part of the process
going. A few things I thought I would mention though...
1. At first when I tried to do the -nuintensitycor command it was
saying it found no data in /mri (no orig.mgz file there). When I did
mksubjdirs, it made folders for al
hi Dave-
it sounds like you may be skipping some steps.
what volume do you currently have? the order of the volumes to be created
is:
orig->nu->T1->brain->wm
the -segmentation step only runs the brain->wm step.
if you have an orig volume, use either:
-stage1
or:
-nuintensitycor -normalization
Not sure what's going on there. You may have gotten into a situation
where some of the processing was done in COR and some im MGZ. It will
assume to do things in mgz unless you specify -COR.
One thing you can do to get things synched back up is to convert all
your CORs to mgzs, eg,
cd mri
It automatically tries to figure out what format you use for your
analysis. It looks for mri/orig/XXX.mgz (which XXX is anything between
0-9). If it does not find that, it assumes COR. Specify -mgz to force mgz.
David Soscia wrote:
hey guys,
Im trying to process an orig scan from the term
