I'm running autorecon2 and i forgot to turn off the setting on my computer that automatically stalls any processes that are going at the time and asks for a log-in password when the computer sits idle for a while. I logged back in and it appears autorecon2 has stalled because of this. The command line is still there with all of the information from what has already been done in autorecon2...is there a way to resume what it was doing from this exact point and not have to start it over?
thanks dave
there are options to recon-all to run any set of individual steps, but this seems more trouble than it's worth. Just rerun it would be my advice.
Bruce On Tue, 13 Jun 2006 dasoscia@buffalo.edu wrote:
I'm running autorecon2 and i forgot to turn off the setting on my computer that automatically stalls any processes that are going at the time and asks for a log-in password when the computer sits idle for a while. I logged back in and it appears autorecon2 has stalled because of this. The command line is still there with all of the information from what has already been done in autorecon2...is there a way to resume what it was doing from this exact point and not have to start it over?
thanks dave _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
my terminal screen has been sitting on this for about an hour...is this normal or does it look like something is stuck?
**************** pass 1 of 1 ************************ setting smoothness coefficient to 0.01 blurring input image with Gaussian with sigma=2.000... pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased switching integration type to fixed (done=0) pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change < tol 0.025, nsmall = 2 of 2 switching integration type to fixed (done=1) rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 blurring input image with Gaussian with sigma=0.500... pct change decreased switching integration type to fixed (done=0) pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct chang
that's the (not very informative) output of the nonlinear volume morph. It can take a day depending on your hardware, so expect it to go on for a while. I'll try to make the output a bit more interesting.
On Tue, 13 Jun 2006 dasoscia@buffalo.edu wrote:
my terminal screen has been sitting on this for about an hour...is this normal or does it look like something is stuck?
**************** pass 1 of 1 ************************ setting smoothness coefficient to 0.01 blurring input image with Gaussian with sigma=2.000... pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased switching integration type to fixed (done=0) pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change < tol 0.025, nsmall = 2 of 2 switching integration type to fixed (done=1) rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 blurring input image with Gaussian with sigma=0.500... pct change decreased switching integration type to fixed (done=0) pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct chang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This is normal. mri_ca_register can take 10 hours. To see if it is still running, open another terminal and type top, you should see all the running processes. Check http://surfer.nmr.mgh.harvard.edu/fswiki/recon_2dall to see approximate run times for each step. Mike
dasoscia@buffalo.edu wrote:
my terminal screen has been sitting on this for about an hour...is this normal or does it look like something is stuck?
**************** pass 1 of 1 ************************ setting smoothness coefficient to 0.01 blurring input image with Gaussian with sigma=2.000... pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased switching integration type to fixed (done=0) pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change < tol 0.025, nsmall = 2 of 2 switching integration type to fixed (done=1) rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 blurring input image with Gaussian with sigma=0.500... pct change decreased switching integration type to fixed (done=0) pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct chang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
dasosciaï¼ buffalo.edu -
Michael Ho