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 <ldw70...@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_344 79/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_344 79/mri/transforms/cc_up.lta reading aseg from /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_344 79/mri/aseg.auto_noCCseg.mgz reading norm from /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_344 79/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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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