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
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
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
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 CautionHello 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>&1Waiting 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
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
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 CautionHi 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 wasthe
full job output? What is in the recon-all.log? Does this happen ifyou
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). Thecommon error
> between all of them is this line > > Waiting for PID 2778 of (2778 2781) to complete... > /usr/local/freesurfer/bin/reconbatchjobs: line 81: 2778Segmentation 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, Iveattached the
> recon-all.log in case it's of any use. > I have checked the log but I dont find de cause. > > 1) FreeSurferversion: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
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 CautionHi 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 CautionHi 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
freesurfer@nmr.mgh.harvard.edu