recon-all -s SOME_SUBJECT exited with ERRORS

List overview All Threads
Download

newer

older

Version 5.3 vs. Version 6

Help with "orig.mgz"

Emanuel Alvaredo

1 Oct 2019 1 Oct '19

4:07 p.m.

External Email - Use Caution

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-v6.0.0-2beb96c 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 Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached

Thanks in advance Emanuel

Attachments:

attachment.html (text/html — 1.3 KB)
recon-all.log (text/x-log — 214.1 KB)

Show replies by date

Emanuel Alvaredo

30 Oct 30 Oct

9:36 a.m.

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.

FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz

uname -a: Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all.log: see attached

Thanks in advance Emanuel

Bruce Fischl

9:51 a.m.

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.

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

Emanuel Alvaredo

7 Nov 7 Nov

1:11 p.m.

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.

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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Bruce Fischl

2:39 p.m.

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
  >
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Emanuel Alvaredo

10:23 p.m.

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
  >
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Bruce Fischl

10:50 p.m.

Sure, if you have enough ram and cores

...

On Nov 7, 2019, at 10:23 PM, Emanuel Alvaredo ealvaredo@gmail.com wrote:
    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
  >
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2398

Age (days ago)

2436

Last active (days ago)

freesurfer@nmr.mgh.harvard.edu

6 comments

2 participants

tags (0)

participants (2)

Bruce Fischl
Emanuel Alvaredo