Hello All,
I have a number of jobs that I will be running through recon-all-nmr -stage1 in the next few days. I tried using the -disable-autoseg flag, but it seems not to work as the jobs I submitted this morning have now run for 50 minutes.
The command line as I typed it was
pbsubmit -c "recon-all-nmr -stage1 -subjid $s -nuintensitycor -usenuintensitycor -disable-autoseg"
perhaps I've misplaced the flag? If anyone has any insight as to why it seems to be persitting in running the autoseg I would appreciate it.
Thanks! Eliz
I think you need to put -disable-autoseg in front of -stage1.
-Xiao
On Tue, 7 Jun 2005, Elizabeth Fenstermacher wrote:
Hello All,
I have a number of jobs that I will be running through recon-all-nmr -stage1 in the next few days. I tried using the -disable-autoseg flag, but it seems not to work as the jobs I submitted this morning have now run for 50 minutes.
The command line as I typed it was
pbsubmit -c "recon-all-nmr -stage1 -subjid $s -nuintensitycor -usenuintensitycor -disable-autoseg"
perhaps I've misplaced the flag? If anyone has any insight as to why it seems to be persitting in running the autoseg I would appreciate it.
Thanks! Eliz
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm pretty sure that I have gotten it to work successfully placing the flag after -stage1. Eliz, are you using a frozen version for this? the flag wasn't working for a while, it was fixed recently, last week or so. I'd suggest you run this if you are using an old frozen version:
recon-all-nmr -stage1 -nosubcortseg -nuintensitycor -usenuintensitycor -subjid $s
Jenni
On Tue, 7 Jun 2005, Xiao Han wrote:
I think you need to put -disable-autoseg in front of -stage1.
-Xiao
On Tue, 7 Jun 2005, Elizabeth Fenstermacher wrote:
Hello All,
I have a number of jobs that I will be running through recon-all-nmr -stage1 in the next few days. I tried using the -disable-autoseg flag, but it seems not to work as the jobs I submitted this morning have now run for 50 minutes.
The command line as I typed it was
pbsubmit -c "recon-all-nmr -stage1 -subjid $s -nuintensitycor -usenuintensitycor -disable-autoseg"
perhaps I've misplaced the flag? If anyone has any insight as to why it seems to be persitting in running the autoseg I would appreciate it.
Thanks! Eliz
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
use the one in dev not std env
Elizabeth Fenstermacher wrote:
Hello All,
I have a number of jobs that I will be running through recon-all-nmr -stage1 in the next few days. I tried using the -disable-autoseg flag, but it seems not to work as the jobs I submitted this morning have now run for 50 minutes.
The command line as I typed it was
pbsubmit -c "recon-all-nmr -stage1 -subjid $s -nuintensitycor -usenuintensitycor -disable-autoseg"
perhaps I've misplaced the flag? If anyone has any insight as to why it seems to be persitting in running the autoseg I would appreciate it.
Thanks! Eliz
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Elizabeth Fenstermacher -
Jenni Pacheco -
Xiao Han