Hi all, I'm having a similar issue to the one described below - the mri_cc step seems stuck and goes on for days (still going); I'm using FreeSurfer version 5.1 as well. Like Bruce said in another thread, this could be due to an empty norm.mgz file. This seems like it is my exact problem, as that file is empty. Is there a way to skip this step, or to re-run from autorecon1 and ensure the norm.mgz file is created?
Thanks, Adam *Adam Mezher* Staff Research Associate II Center for Imaging of Neurodegenerative Diseases San Francisco VA Medical Center 4150 Clement St. (114M) San Francisco, CA 94121 Tel: 415-221-4810 Ext. 4629 Fax: 415-668-2864 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 at ma-tea.com <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> 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 at gmail.com <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> *>* Date: Wednesday, February 20, 2013 10:49 AM *>* To: <freesurfer at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> *>* 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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