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
hey guys,
Now I am getting this error when trying to process the volume:
[EMAIL PROTECTED] 1768-4]$ recon-all -subjid 1768-4 -mgz -segmentation
INFO: SUBJECTS_DIR is /home/amc/freesurfer_new/freesurfer/subjects
program versions used
$Id: recon-all-nmr,v 1.
