hmmm, does it always happen for this subject? What if you don't use
-parallel?
On Thu, 7 Nov 2019, Emanuel Alvaredo wrote:

>
>         External Email - Use Caution        
>
> Hi Bruce! Thanks for answer!!
> * The command line is 
>
>  recon-all -s SUBJECT_NAME -i
> /patients/SUBJECT_NAME/2_COGNITIVO/4_Accelerated_Ax_IR-FSPGR/i1602413.MRDC.127 -all -parallel
>
>
>
> * In this mail is attached  the log. There is 
>
> Segmentation fault (core dumped)
>
> * This happens running when I call a process from a Java application, but too if I run the
> command manually.
>
>
>
> I think this is the problem, but I dont know why.
>
> Thanks in advance
>
>
> Emanuel
>
>
> On Wed, Oct 30, 2019 at 10:51 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>       Hi Emanuel
>
>       can you give us more details. What was your command line? What was the
>       full job output? What is in the recon-all.log? Does this happen if you
>       run directly instead of through some type of batch server?
>
>       cheers
>       Bruce
>       On Wed, 30 Oct
>       2019, Emanuel Alvaredo wrote:
>
>       >
>       >         External Email - Use Caution        
>       >
>       > Hello Developers!
>       > I am getting the same error in several patients (not all). The common error
>       > between all of them is this line
>       >
>       > Waiting for PID 2778 of (2778 2781) to complete...
>       > /usr/local/freesurfer/bin/reconbatchjobs: line 81:  2778 Segmentation fault
>       >      (core dumped) exec $JOB >> $LOG 2>&1
>       > Waiting for PID 2781 of (2778 2781) to complete...
>       >
>       > Any idea? 
>       >
>       > Thanks in advance!
>       >
>       >
>       >
>       > Emanuel
>       >
>       >
>       > On Tue, Oct 1, 2019 at 5:07 PM Emanuel Alvaredo <ealvaredo@gmail.com> wrote:
>       >
>       > Hello FreeSurfer Developers,
>       >
>       > I am running de following command
>       > /usr/local/freesurfer/subjects/SOME_SUBJECT
>       > /usr/local/freesurfer/bin/recon-all
>       > -s SOME_SUBJECT -i /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_
>       > FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 -
>       > all -parallel
>       > I've searched the list and no similar errors have been reported. Does anyone
>       >  have any thoughts on how to trouble-shoot this one? Also, Ive attached the
>       > recon-all.log in case it's of any use.
>       > I have checked the log but I dont find de cause.
>       >
>       > 1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb
>       > 96c
>       > 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
>       > 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu S
>       > ep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>       > 4) recon-all.log: see attached
>       >       Thanks in advance
>       > Emanuel
>       >
>       >
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