Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS

External Email - Use Caution

Hi Bruce, same result.

Question, Is it possible run two recon-all at the same time?

Emanuel

On Thu, Nov 7, 2019 at 4:41 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

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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