See my original post at the end of this message and some more information included below.
What would have been edited between the previous run without errors and the current run with errors is the brainmask, the wm.mgz file, and control points.
On Tue, Oct 30, 2012 at 1:21 PM, Christine Smith cnsmith@ucsd.edu wrote:
Here it is:
New invocation of recon-all
Thu Oct 4 03:52:22 PDT 2012 /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 /usr/local/freesurfer/bin/recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel #-------------------------------------- #@# SubCort Seg Thu Oct 4 03:52:22 PDT 2012
mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz
Linux squirelab.ucsd.edu 2.6.18-308.13.1.el5 #1 SMP Tue Aug 21 18:44:22 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s CON1 exited with ERRORS at Thu Oct 4 03:52:22 PDT 2012
On Tue, Oct 30, 2012 at 12:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what were the last 20 lines or so of the recon-all.log?
On Tue, 30 Oct 2012, Christine Smith wrote:
Hello,
After successfully running a subject through freesurfer (recon-all -make all) several times as I fixed some pial and white matter edits, I now get the message that recon-all finished with errors. Inspection of the recon-all.log doesn't reveal any error messages to me in any particular step.
What should I be looking for to track down the reason that errors were generated?
I already examined the talairach transform and that looks great. I loaded the pial and white matter surfaces and they look fine. The segmentation aparc+aseg looks great too.
Thanks, Christine