a whole night may not be enough depending on the speed of your machine, and how far from our atlas anatomy your subject is. Those messages are normal and part of the most computationally intensive step in recon-all, so see if it take a day or so to finish
On Wed, 7 Mar 2012, Jimmy Ghaziri wrote: > I waited a whole night ... I don't recall getting this message last summer.I > will run it again and check it back again on Friday just to be sure. > > Thank you, > > Jimmy > > On Wed, Mar 7, 2012 at 15:44, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > 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 > > > > > 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. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
