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