Hi Bruce, Sorry to get back late on this. The norm file was blank.
Can you send me the updated binary??, My system specification is following: Red Hat Enterprise LINUX Workstation Release 6.0 (Santiago) Kernel Linux 2.6.37-71.el6.x86_64 GNOME 2.28.2 Also, just for information this is not going to affect any output (I was looking for cortical thickness), right? And if I use version 5.3, Will that going to affect any of the output (if you already know them..) that I get from FS 5.1.0? Please let me know. Thanks! ~Siddharth -----Original Message----- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 2:26 PM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] F Problem running : mri_cc -aseg.auto_ Hi Siddharth can you cc the list so others can answer? Did you check the norm to make sure it's ok? You can definitely take the mri_cc from 5.3 and use the rest of 5.1. If you let us know your hardware/software environment we'll send you an updated binary, but as I said it's usually a symptom of something else going wrong Bruce On Thu, 16 May 2013, Ray, Siddharth wrote: > Hi Bruce, > > Thanks for the prompt reply. I am using 5.1 version and I don’t think I can > switch to a new version because I already have subjects processed using this > one. > > So do we have any fix for this version? > > Please let me know. > > -Siddharth > > -----Original Message----- > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: Thursday, May 16, 2013 2:08 PM > To: Ray, Siddharth > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] F Problem running : mri_cc -aseg.auto_ > > Hi Siddharth > > what FS version are you running? I did fix this recently, and the fix > is certainly in 5.3. It only happened if there was something badly > wrong, like the norm.mgz being empty for example, so it was more a > symptom of an earlier failure then a problem of it's own (although I > did have it print out an error message instead of running forever) > > > cheers > Bruce > > On Thu, 16 May 2013, Ray, > Siddharth wrote: > >> >> Hi, >> >> >> >> I am new to freesurfer and was trying to run it on couple of my >> subjects but I am stuck (for last 40 hrs) at stage >> >> >> >> “mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta >> /home/sray2/Desktop/combirx/cr052_ip_output/mri/transforms/cc_up.lta >> cr052_ip_output” >> >> >> >> it seems. The last few lines of the log file were: >> >> >> >> searching scale 1 Z rot 9.9 >> >> searching scale 1 Z rot 10.1 global minimum found at slice 122.0, >> rotations (-3.99, 3.36) >> >> final transformation (x=122.0, yr=-3.992, zr=3.355): >> >> 0.996 -0.059 -0.069 25.704; >> >> 0.058 0.998 -0.004 -3.212; >> >> 0.070 0.000 0.998 -51.078; >> >> 0.000 0.000 0.000 1.000; >> >> >> >> >> >> Have anyone came across this error before ? and know how to fix this. >> Please let me know. >> >> >> >> Thanks in advance. >> >> >> >> ~Siddharth Ray >> >> >> >> P.S. I have attached the log file here. >> >> >> > > > 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. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
