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