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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
the labels are deprecated since we have the cortical parcellation. And yes, run parcellate_subject and it will create *.annot files in the label dir. cheers, Bruce
On Wed, 8 Jun 2005, Fornito, Alexander wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think it looks in the average7 directory for a few labels (central sulc, calc, ...), then maps them to your subject through the registration. The intent was that you could then look at these labels to make sure they were in about the right place.
doug
Bruce Fischl wrote:
the labels are deprecated since we have the cortical parcellation. And yes, run parcellate_subject and it will create *.annot files in the label dir. cheers, Bruce
On Wed, 8 Jun 2005, Fornito, Alexander wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Fornito, Alexander