Dear Freesurfer experts,

I am running autorecon2 using Freesurfer verion 5.1.0 on Linux. For some subjects, it looks that the pipeline stucked in the middle of  mri_cc and keeps running for days (without any error message). Last time when it occurred I thought it may be caused by some hardware-related problem, so I killed these jobs and re-launched recon-all -autorecon2 on a different machine. Now these jobs have been running for over 40 hours and they are still running. Do you know why they take so long? For your reference,  I copied the most recent processing information below:  

mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/transforms/cc_up.lta 0057_34479

will read input aseg from aseg.auto_noCCseg.mgz

writing aseg with cc labels to aseg.auto.mgz

will write lta as /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/transforms/cc_up.lta

reading aseg from /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/aseg.auto_noCCseg.mgz

reading norm from /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/norm.mgz

24076 voxels in left wm, 23641 in right wm, xrange [73, 130]

searching rotation angles z=[65 79], y=[-54 -40]

searching scale 1 Z rot 75.6  global minimum found at slice 103.0, rotations (-50.09, 68.60)

final transformation (x=103.0, yr=-50.093, zr=68.597):

0.234  -0.931  -0.280   230.831;

0.597   0.365  -0.714   75.219;

0.767  -0.000   0.642   3.440;

0.000   0.000   0.000   1.000;

Thanks in advance for your help!

Dawei