That worked, thanks, Doug. To expand on the labels issue, from my understanding, the labels are used to check that the registration worked, and that these are automatically created. I don't have any files in my labels directory. Do you need to run parcellate_subject to get them? Is there any documentation on parcellate_subject? I tried to run it and got the message: CSURF_DIR: Undefined variable.
as an aside, where is the average7 surface. I though it might be in /usr/local/freesurfer/average/, but I don't seem to be able to open any of the files in there with tksurfer. Thanks again, Alex
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Wed 6/8/2005 11:08 AM To: Elizabeth Fenstermacher Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all-nmr -disable-autoseg 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
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