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 matt@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 ldw70171@gmail.com Date: Wednesday, February 20, 2013 10:49 AM To: freesurfer@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

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