Hi Siddharth

what FS version are you running? I did fix this recently, and the fix is certainly in 5.3. It only happened if there was something badly wrong, like the norm.mgz being empty for example, so it was more a symptom of an earlier failure then a problem of it's own (although I did have it print out an error message instead of running forever)

cheers Bruce

On Thu, 16 May 2013, Ray, Siddharth wrote:

Hi,

I am new to freesurfer and was trying to run it on couple of my subjects but I am stuck (for last 40 hrs) at stage

“mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/sray2/Desktop/combirx/cr052_ip_output/mri/transforms/cc_up.lta cr052_ip_output”

it seems. The last few lines of the log file were:

searching scale 1 Z rot 9.9

searching scale 1 Z rot 10.1  global minimum found at slice 122.0, rotations (-3.99, 3.36)

final transformation (x=122.0, yr=-3.992, zr=3.355):

0.996  -0.059  -0.069   25.704;

0.058   0.998  -0.004  -3.212;

0.070   0.000   0.998  -51.078;

0.000   0.000   0.000   1.000;

Have anyone came across this error before ? and know how to fix this. Please let me know.

Thanks in advance.

~Siddharth Ray

P.S. I have attached the log file here.