On Wed, Mar 7, 2012 at 15:44, Bruce Fischl <fischl@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

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