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 <fis...@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 <fis...@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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