Hi Bruce,

Thanks for the reply, below is a couple of sentences from the recon-all.log

reading initial pial vertex positions from white.preaparc...

mean border=65.6, 300 (300) missing vertices, mean dist 2.2 [2.0 (%0.1)->3.2 (%99.9))]

%21 local maxima, %44 large gradients and %29 min vals, 639 gradients ignored

perforing initial smooth deformation to move away from white surface

tol=1.0e-04, sigma=2.0, host=hpc17, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000

mom=0.00, dt=0.05.

I also attached a screenshot of the log.

Is there a place I should upload the files?

Thanks,

Jasmin

On Wed, May 31, 2017 at 12:28 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Jasmin

typically that means there is a big topological defect, which definitely can be caused by motion. What is the last couple of lines of the recon-all.log file of one of the subjects? Can you upload an image we can look at?

cheers
Bruce

On Wed, 31 May 2017, Jasmin Alves wrote:

Hello,
I have used FS6.0 to do recon-all on about 57 brains, but for some reason,
recon-all is not working on some brains, recon-all is not able to get past
"Automatic topology fixer", after the command has been running for 24 hours.

Is it possible there is too much motion in the image? Or does FS6.0
possibly take longer to complete for some brains?

Thanks,
Jasmin

--
Jasmin Alves
Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jalves@usc.edu

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