Hi Adam yes, this is mri_cc in an infinite loop. This bug is fixed in 5.3, but it won't generate anything reasonable with an empty input volume. Do you know why it is blank? Is the brainmask.mgz ok? The talariach.lta and .xfm?
cheers Bruce On Fri, 6 Dec 2013, Adam Mezher wrote: > 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 <MailScanner has detected a possi > ble 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 get > s 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 "m > ail.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 s > ubjects, it looks that the pipeline stucked in the middle of mri_cc and kee > ps 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 the > se jobs and re-launched recon-all -autorecon2 on a different machine. Now th > ese 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 recen > t processing information below: > > > > > > > > mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Experiments/2012 > 0801.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, rotatio > ns (-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.
