Hi Jimmy that isn't an error message - just an informational one. How long did you wait? Are you sure it is not going to terminate if you let it run long enough?
cheers Bruce On Wed, 7 Mar 2012, Jimmy Ghaziri wrote: > Dear FreeSurfer community, > > I am running Ubuntu 11.10 on an Intel i7 970 3.20Ghz 64bit (11 CPUs) with > 12GB DDR3 RAM on a 120GB raid 0 solid state hard drives. > I have ran recon-all this summer on some of my subjects and it worked > perfectly in 13 hours. > > I'm trying to run one more analyse (a recon-all) and I keep getting this > error message when it gets to recon2 : > > **************** pass 1 of 1 ************************ > setting smoothness coefficient to 0.039 > blurring input image with Gaussian with sigma=2.000... > 0000: dt=0.000, rms=0.789, neg=0, invalid=766 > gcamFindOptimalTimeStep: Complete in 26136.459 ms > 0001: dt=129.472000, rms=0.731 (7.421%), neg=0, invalid=766 > gcamFindOptimalTimeStep: Complete in 24108.512 ms > > and it continues this way on and on. > > > I tried to run recon-all again on an old subject (on which it worked this > summer) by renaming the files and folders of course and I got the same > error message. I uninstalled and reinstalled FreeSurfer and still am getting > the message. > I ran one of the subject on my colleagues machine (which is slower than mine; > took him 22 hours) and it worked perfectly. > > Can anyone tell me what could be the problem ? I will need to run more > analyses in a few months and I need to fix it ASAP. > > Here's the command I'm using (which is the same as my colleague and as > indicated on FS wiki) : > > recon-all -subjid a_al_t1 -i > ~/Documents/T1W_3D_TFE/GHA_A-C_2234495-T1W_3D_TFE-20101207-301-1.dicom -all > > > Thank you, > > Jimmy > > _______________________________________________ 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.
