yes, probably
On Wed, 14 Aug 2013, Eli Fredman wrote:
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/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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