Yes it is still at defect 32.

The tail of the recon-all.log is as follows:

CORRECTING DEFECT 30 (vertices=18, convex hull=22)
After retessellation of defect 30, euler #=-7 (59491,172395,112897) : difference with theory (-28) = -21

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)


Should I attach the lh.inflated.nofix in a separate email to you, Bruce?



On Tue, Feb 26, 2013 at 10:08 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
is it still on defect 32? What does the tail of the recon-all.log say? And can you send us an image of the lh.inflated.nofix (if it is the lh that is running)?


On Tue, 26 Feb 2013, Blessy M wrote:

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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