I verified lh.orig.nofix, and it looks fine. But, there has been no new files created since Saturday (2/23/2013).

I am considering stopping the process.

I was thinking, I had created a skull stripped image, and was giving that as input to recon-all in the command below:
recon-all -subjid . -noskullstrip -autorecon1 -notal-check -autorecon2
            -autorecon3

Should -noskullstrip flag be after autorecon1?



On Mon, Feb 25, 2013 at 3:35 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
try looking at the lh.inflated.nofix or lh.orig.nofix (or rh, whichever one is running) and see if something is dramatically wrong (like skull attached to brain, or hemis connected, etc....)

On Mon, 25 Feb 2013, Blessy M wrote:

Recon is still running. I started the process on 2/21/2013. Its been 4 days.

I ran this command, and viewed the aseg file, and that looks reasonable
tkmedit ./ brainmask.mgz -aux T1.mgz -surfs -aseg

Currently it is at this stage:

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 13 iterations
marking ambiguous vertices...
124766 ambiguous faces found in tessellation
segmenting defects...
......

61 defects to be corrected
0 vertices coincident
......
......
CORRECTING DEFECT 31 (vertices=244, convex hull=142)
After retessellation of defect 31, euler #=-6 (59502,172495,112987) : difference with theory (-27) = -21

CORRECTING DEFECT 32 (vertices=44865, convex hull=8969)








On Fri, Feb 22, 2013 at 5:33 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
      I don't think either one of these are errors, just warnings that occur pretty frequently and I don't think should
      impact the results. Does the recon finish? Do the results look ok?

      On Fri, 22 Feb 2013, Blessy M wrote:


            I am getting the bottom two sets of errors while doing a simple recon-all.

            More specifically while running this command:
            recon-all -subjid . -noskullstrip -autorecon1 -notal-check -autorecon2
            -autorecon3

            Has someone encountered this kind of errors? Is there a fix?

            1)
            Computing MAP estimate using 2772 samples...
            ********************************************
            IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
            RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
            INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) =
            7296.5  tol 0.000010
            ...
            ...

            2)
             unfolding failed - restoring original position --------------------
            0146: dt=13.779160, rms=0.814 (0.000%), neg=0, invalid=766
            blurring input image with Gaussian with sigma=0.500...
            0000: dt=0.000, rms=0.814, neg=0, invalid=766
            gcamFindOptimalTimeStep: Complete in 101542.133 ms
            iter 0, gcam->neg = 801

            ......................

            unfolding failed - restoring original position --------------------
            0158: dt=13.828393, rms=0.814 (-0.069%), neg=0, invalid=766
            blurring input image with Gaussian with sigma=0.500...
            0000: dt=0.000, rms=0.814, neg=0, invalid=766
            gcamFindOptimalTimeStep: Complete in 100610.148 ms





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