Thanks for the quick response Bruce. Is that missing patch the reason that it did not create a wmparc.mgz file in any of our cases?
On Wed, Aug 14, 2013 at 10:47 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Eli > > I don't think that's an error, just an arcane warning that some open > source numerical minimization code complains about sometimes. Looking at > the log it seems like it completed ok, although this is the version of 5.3 > without the segstats/ribbon patch, which you will probably want to download > (can someone point Eli at this?) > > cheers > Bruce > > > > > > On Wed, 14 Aug 2013, Eli Fredman wrote: > > 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/01** >> 409-t1w-realign-masked.ni <http://01409-t1w-realign-masked.ni> >> i.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! >> >> -- >> Eli Fredman, BA >> Research Assistant >> Psychiatry Neuroimaging Laboratory >> Harvard Medical School, Brigham and Women's Hospital >> 1249 Boylston St, 3rd Floor >> Boston, MA 02215 >> Office: (617) 525-6118 >> Cell: (314) 952-8098 >> Fax: (617) 525-6150 >> >> -- Eli Fredman, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6118 Cell: (314) 952-8098 Fax: (617) 525-6150
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