I ran 10 cases through freesurfer5.3 last night and found that they all exited with the same error. This is the input that I used:
recon-all -i /projects/schiz/NFL/case01409/strct/align-space/01409-t1w-realign-masked.nii.gz -autorecon1 -noskullstrip -subjid 01409 && cp subjects/01409/mri/T1.mgz subjects/01409/mri/brainmask.mgz && recon-all -autorecon2 -subjid 01409 && recon-all -autorecon3 -subjid 01409
I've attached the recon-all.log file which shows the following error:
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 TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010
(as a side note, the reason I don't simply run recon-all -all is because this doesn't seem to acknowledge the -noskullstrip tag).
Thanks for the help!