Hi Saad, Since there is no message indicating it stopped due to error, I would try running it again as it most likely stopped due to the machine it was running on. You can pick up where it left off by doing: recon-all -make all -s mysubject
On Apr 7, 2011, at 12:25 AM, Saad Ramadan <saad.rama...@gmail.com> wrote: > Dear all, > > > I ran (on an isotropic MPRAGE ): > > recon-all -subject mysubject -i > ./DICOM/test.25.1.2010.04.27.21.51.18.31250.14004670.IMA -autorecon-all > > which ran for few hours and then exited without a successful end as can be > seen on log file below. > > > Contents of recon-all-status.log are: > > Wed Apr 6 12:31:55 EDT 2011 > #@# MotionCor Wed Apr 6 12:33:10 EDT 2011 > #@# Nu Intensity Correction Wed Apr 6 12:33:40 EDT 2011 > #@# Talairach Wed Apr 6 12:35:22 EDT 2011 > #@# Talairach Failure Detection Wed Apr 6 12:36:53 EDT 2011 > #@# Intensity Normalization Wed Apr 6 12:36:53 EDT 2011 > #@# Skull Stripping Wed Apr 6 12:41:44 EDT 2011 > #@# EM Registration Wed Apr 6 14:16:04 EDT 2011 > #@# CA Normalize Wed Apr 6 15:18:54 EDT 2011 > #@# CA Reg Wed Apr 6 15:22:59 EDT 2011 > > The last few lines of recon-all.log produces: > > 0091: dt=0.112000, rms=0.700 (-0.001%), neg=0, invalid=766 > resetting metric properties... > setting smoothness coefficient to 10.00 > blurring input image with Gaussian with sigma=2.000... > 0000: dt=0.000, rms=0.638, neg=0, invalid=766 > 0092: dt=0.772947, rms=0.623 (2.335%), neg=0, invalid=766 > 0093: dt=0.028000, rms=0.622 (0.145%), neg=0, invalid=766 > 0094: dt=0.028000, rms=0.622 (-0.063%), neg=0, invalid=766 > blurring input image with Gaussian with sigma=0.500... > 0000: dt=0.000, rms=0.622, neg=0, invalid=766 > > > Do you have any idea what is going wrong here? > > Thanks > _______________________________________________ > 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
