I've noticed this at well when something goes wrong before mri_cc. It gets stuck in some kind of infinite loop. You might check that the linear and nonlinear registration worked correctly.

If someone can send us and example of this behavior I will fix it
Cheers
Bruce

On Feb 20, 2013, at 12:23 PM, Matt Glasser <MailScanner has detected a possible fraud attempt from "mail.nmr.mgh.harvard.edu" claiming to be matt at ma-tea.com> wrote:

> I've noticed this at well when something goes wrong before mri_cc.  It gets stuck in some kind of infinite loop.  You might check that the linear and nonlinear registration worked correctly.
> 
> Peace,
> 
> Matt.
> 
> From: Dawei Liu <MailScanner has detected a possible fraud attempt from "mail.nmr.mgh.harvard.edu" claiming to be ldw70171 at gmail.com>
> Date: Wednesday, February 20, 2013 10:49 AM
> To: <freesurfer at nmr.mgh.harvard.edu>
> Subject: [Freesurfer] unusually long running time in autorecon2
> 
> 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