the log does not indicate that mri_em_register exited with an error. it appears that it produced its output correctly and continued through to nearly the end of the stream. the IFLAG messages can be ignored.
the log indicates that mri_label2label is exiting with an error when trying to load the label from the fsaverage directory. the fsaverage subject is symlinked to the users SUBJECTS_DIR (to save space), but sometimes this seems to cause problems on some systems. i would try copying it to your subjects dir: cd $SUBJECTS_DIR rm fsaverage cp -r $FREESURFER_HOME/subjects/fsaverage . then you just need to run the last two stages of recon-all: recon-all -s <subjid> -balabels -label-exvivo-ec or if you dont care about the Brodmann or exvivo EC labels, you dont need to run anything. for reference: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable n. On Wed, 2011-09-28 at 17:36 -0400, Warren Winter wrote: > Hi Nick, > > > Thanks for your help. > > > The first set of errors (of the kind I described) follows the command > " mri_em_register -skull > nu.mgz > /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_withskull_2008-03-26.gca > transforms/talairach_with_skull.lta " > > > The next follows the command " mri_em_register -uns 3 -mask > brainmask.mgz > nu.mgz > /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_2008-03-26.gca > transforms/talairach.lta" > > > The next follows the command " mri_em_register -skull -t > transforms/talairach.lta > nu_noneck.mgz > /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_withskull_2008-03-26.gca > transforms/talairach_with_skull_2.lta " > > > I've attached the log if you could use it for reference. > > > Best, > > > Warren > > > > > > On Sep 28, 2011, at 4:18 PM, Nick Schmansky wrote: > > > the IFLAG messages can be ignored if mri_em_register is not exiting > > with > > error. which command is running that is exiting with error? can > > you > > send that command line from the recon-all.log file? > > > > n. > > > > On Wed, 2011-09-28 at 16:02 -0400, Warren Winter wrote: > > > Hi, > > > > > > > > > Each time I have run recon-all on our subjects, I end up with the > > > same > > > slew of error messages underneath "Computing MAP estimate using [x > > > number of] samples" and underneath "EM alignment process": > > > > > > > > > "IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE > > > MCSRCH > > > ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR > > > GRADIENT ARE INCORRECT OR INCORRECT TOLERANCES" > > > > > > > > > At the very end of the log file I see: > > > > > > > > > "Loading source label. > > > Abort > > > Linux rc-twice 2.6.39.2-mosix #1 SMP Wed Jun 29 11:53:08 EDT 2011 > > > x86_64 x86_64 x86_64 GNU/Linux > > > > > > > > > recon-all -s 5 exited with ERRORS at Tue Sep 27 03:23:46 EDT 2011" > > > > > > > > > Any help on this would be greatly appreciated. > > > > > > > > > Best, > > > > > > > > > Warren > > > > > > -- > > > Warren Winter > > > Lab Coordinator > > > Children's Hospital Boston > > > Division of Developmental Medicine > > > 1 Autumn Street, AU 650 > > > Boston, MA 02215 > > > 857-218-5224 > > > > > > > > > _______________________________________________ > > > 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. > > > > > > > -- > Warren Winter > Lab Coordinator > Children's Hospital Boston > Division of Developmental Medicine > 1 Autumn Street, AU 650 > Boston, MA 02215 > 857-218-5224 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
