Hi,
I have an image with very large ventricles, which makes the stripping step
of the algorithm to fail. I have the stripped version of the image and was
trying to use -noskullstrip flag to just input the stripped image. But I got
an error of "could not open mask volume brainmask.mgz". Would you p
Hi All,
I'm running freesurfer on a public station, so I need to sign out when I'm
finished with sessions. Has anyone found a suitable way to run freesurfer
in the background? I know that I can run matlab in the background here, so
if there is a way to run the pipeline through matlab that may wo
This tip comes from Sam at the helpdesk...
At the command prompt, type 'screen' and press enter. This opens the
terminal emulation program, aptly named screen. In this new terminal, start
your recon as you would normally, whether that's invoking a script of your
making or typing in the standard
You can also just run e.g. "nohup recon-all -autorecon-all -s doe_j &"
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Scott Burns
[sbu...@nmr.mgh.harvard.edu]
Sent: Tuesday, December 14, 2010 8:05 PM
To:
You can make it work with nohup? In the past I've had trouble and my
thinking was that because recon-all starts many child processes, the
currently continues after the terminal is closed, but any subsequent
process can't start. That's why I've been using screen, but YMMV.
Scott Burns
Kuperberg
I should have clarified. I use nohup when I ssh into my workstation from
elsewhere. I haven't tried it in which I would have to log out from the machine
running recon-all.
From: Scott Burns [sbu...@nmr.mgh.harvard.edu]
Sent: Tuesday, December 14, 2010 9:54
Thanks, this is very helpful
On Tue, Dec 14, 2010 at 9:12 PM, Watson, Christopher <
christopher.wat...@childrens.harvard.edu> wrote:
> I should have clarified. I use nohup when I ssh into my workstation from
> elsewhere. I haven't tried it in which I would have to log out from the
> machine runni
Bruce et al,
Did you ever get to the bottom of Joakim's problem? I'm getting the same error.
I checked the talairach and it looks fine. But for some reason mri_normalize
can't find any peaks so T1.mgz comes out as all zeros.
I just uploaded the subject to your anon FTP server.: ex03.2.tgz
Than
