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
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-- Warren Winter Lab Coordinator Children's Hospital Boston Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224