Hi Bruce,
Thanks for the tips. I tried playing around with the files for a bit
but didn’t make much progress.
Here’s a link to the full tar/gz’ed subject dir:
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=4ej948sa49s
Thanks!
Dan
On Fri Jun 24 22:22:17 EDT 2016, Bruce Fischl
wrote:
> Hi Dan
>
> that defect is too big, there must be something wrong. Check to see if the
> surface is connected to dura or across the hemis or something. You can look
> at the lh.inflated.nofix and/or the lh.orig.nofix to see where the defects
> are. Then you'll need to correct something once you've figured out why
> there is such a huge defect.
>
> cheers
> Bruce
>
> p.s. if you can't sort this out you can tar and gzip your whole subject dir
> and we will take a look
>
> On Fri, Jun 24, 2016 at 9:15 PM, Dan Loewenherz
> wrote:
>>
>> Hi freeserver folks,
>>
>> First time poster here. First off, thanks so much to the folks who
>> work on and make this software available to the public. It seems like
>> pretty incredible tech, from what little I understand of it. :)
>>
>> My problem is that the freesurfer process appears to be stuck on the
>> recon-all command. It’s been sitting at ”CORRECTING DEFECT 0
>> (vertices=96285, convex hull=13916)” for about 10 hours now. Any way
>> to cut that number down or should I just let it keep doing its thing?
>> I’ve pasted all of the output pasted at end of the message.
>>
>> Thanks so much!
>>
>> Dan
>>
>> *
>> INFO: assuming .mgz format
>> $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
>> $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
>> before topology correction, eno=-684 (nv=141228, nf=283824,
>> ne=425736, g=343)
>> using quasi-homeomorphic spherical map to tessellate cortical surface...
>>
>> Correction of the Topology
>> Finding true center and radius of Spherical Surface...done
>> Surface centered at (0,0,0) with radius 100.0 in 14 iterations
>> marking ambiguous vertices...
>> 190731 ambiguous faces found in tessellation
>> segmenting defects...
>> 40 defects found, arbitrating ambiguous regions...
>> analyzing neighboring defects...
>> -merging segment 2 into 0
>> -merging segment 5 into 0
>> -merging segment 8 into 0
>> -merging segment 14 into 0
>> -merging segment 25 into 0
>> -merging segment 28 into 0
>> -merging segment 20 into 17
>> -merging segment 29 into 17
>> -merging segment 36 into 35
>> 31 defects to be corrected
>> 0 vertices coincident
>> reading input surface
>> /Applications/freesurfer/subjects/Dan/surf/lh.qsphere.nofix...
>> reading brain volume from brain...
>> reading wm segmentation from wm...
>> Computing Initial Surface Statistics
>> -face loglikelihood: -8.8790 (-4.4395)
>> -vertex loglikelihood: -7.4039 (-3.7020)
>> -normal dot loglikelihood: -3.5029 (-3.5029)
>> -quad curv loglikelihood: -6.1567 (-3.0783)
>> Total Loglikelihood : -25.9425
>>
>> CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)
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