Hi FS experts, I tried to run Tracula with the new FS 5.2 release and came across memory allocation problems in the preprocessing step and would appreciate some advice on solving them:
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice Cannot allocate memory Linux daria-Think 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 i686 i686 i686 GNU/Linux trac-preproc exited with ERRORS at Tue Apr 9 22:21:43 CEST 2013
I attached the log-file. Let me know if you need further information about my system. Thank you in advance, Daria
Hi Daria - How much memory does your system have? Were you ever able to run trac-all from the 5.1 version on the same system?
a.y
On Wed, 10 Apr 2013, Antonenko, Daria wrote:
Hi FS experts, I tried to run Tracula with the new FS 5.2 release and came across memory allocation problems in the preprocessing step and would appreciate some advice on solving them:
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice Cannot allocate memory Linux daria-Think 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 i686 i686 i686 GNU/Linux trac-preproc exited with ERRORS at Tue Apr 9 22:21:43 CEST 2013
I attached the log-file. Let me know if you need further information about my system. Thank you in advance, Daria
Hi Anastasia, I'm running tracula on linux ubuntu (mint 14) on a lenovo thinkpad edge. it has 8gb ram and 4 CPUs, i think it's a lot.. I did not run tracula before on this computer.
Daria
--------------------------------------------- Daria Antonenko, Dipl.-Psych. Charité - Universitätsmedizin Berlin NeuroCure Clinical Research Center NCRC AG Flöel Charitéplatz 1, 10117 Berlin Tel.: +49 30 450 560 223 Fax: +49 30 450 539 921 E-Mail: daria.antonenko@charite.de
-----Ursprüngliche Nachricht----- Von: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 10. April 2013 17:03 An: Antonenko, Daria Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] tracula FS 5.2
Hi Daria - How much memory does your system have? Were you ever able to run trac-all from the 5.1 version on the same system?
a.y
On Wed, 10 Apr 2013, Antonenko, Daria wrote:
Hi FS experts, I tried to run Tracula with the new FS 5.2 release and came across memory allocation problems in the preprocessing step and would appreciate some advice on solving them:
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice Cannot allocate memory Linux daria-Think 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 i686 i686 i686 GNU/Linux trac-preproc exited with ERRORS at Tue Apr 9 22:21:43 CEST 2013
I attached the log-file. Let me know if you need further information about my system. Thank you in advance, Daria
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Daria - It shouldn't need more than 4Gb based on some quick tests that I ran for this particular step where you're getting the memory error. What are the dimensions of your DWI series? Were you running anything else at the same time that was memory-intensive?
a.y
On Thu, 11 Apr 2013, Antonenko, Daria wrote:
Hi Anastasia, I'm running tracula on linux ubuntu (mint 14) on a lenovo thinkpad edge. it has 8gb ram and 4 CPUs, i think it's a lot.. I did not run tracula before on this computer.
Daria
Daria Antonenko, Dipl.-Psych. Charité - Universitätsmedizin Berlin NeuroCure Clinical Research Center NCRC AG Flöel Charitéplatz 1, 10117 Berlin Tel.: +49 30 450 560 223 Fax: +49 30 450 539 921 E-Mail: daria.antonenko@charite.de
-----Ursprüngliche Nachricht----- Von: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 10. April 2013 17:03 An: Antonenko, Daria Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] tracula FS 5.2
Hi Daria - How much memory does your system have? Were you ever able to run trac-all from the 5.1 version on the same system?
a.y
On Wed, 10 Apr 2013, Antonenko, Daria wrote:
Hi FS experts, I tried to run Tracula with the new FS 5.2 release and came across memory allocation problems in the preprocessing step and would appreciate some advice on solving them:
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice Cannot allocate memory Linux daria-Think 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 i686 i686 i686 GNU/Linux trac-preproc exited with ERRORS at Tue Apr 9 22:21:43 CEST 2013
I attached the log-file. Let me know if you need further information about my system. Thank you in advance, Daria
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Anastasia, my first idea was also that something else might disturb the process, but i replicated the error several times and observed the memory load in the system monitor without running anything else, seemed not memory-intensive at all.. I use a 10 b0 + 64dir DTI sequence, 2.3×2.3×2.3 mm3, TR=7500 ms, TE=86 ms. The preprocessing, dtifit and bedpostx with FSL worked fine.
Daria
________________________________________ Von: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Gesendet: Freitag, 26. April 2013 18:38 An: Antonenko, Daria Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW: [Freesurfer] tracula FS 5.2
Hi Daria - It shouldn't need more than 4Gb based on some quick tests that I ran for this particular step where you're getting the memory error. What are the dimensions of your DWI series? Were you running anything else at the same time that was memory-intensive?
a.y
On Thu, 11 Apr 2013, Antonenko, Daria wrote:
Hi Anastasia, I'm running tracula on linux ubuntu (mint 14) on a lenovo thinkpad edge. it has 8gb ram and 4 CPUs, i think it's a lot.. I did not run tracula before on this computer.
Daria
Daria Antonenko, Dipl.-Psych. Charité - Universitätsmedizin Berlin NeuroCure Clinical Research Center NCRC AG Flöel Charitéplatz 1, 10117 Berlin Tel.: +49 30 450 560 223 Fax: +49 30 450 539 921 E-Mail: daria.antonenko@charite.de
-----Ursprüngliche Nachricht----- Von: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 10. April 2013 17:03 An: Antonenko, Daria Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] tracula FS 5.2
Hi Daria - How much memory does your system have? Were you ever able to run trac-all from the 5.1 version on the same system?
a.y
On Wed, 10 Apr 2013, Antonenko, Daria wrote:
Hi FS experts, I tried to run Tracula with the new FS 5.2 release and came across memory allocation problems in the preprocessing step and would appreciate some advice on solving them:
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice Cannot allocate memory Linux daria-Think 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 i686 i686 i686 GNU/Linux trac-preproc exited with ERRORS at Tue Apr 9 22:21:43 CEST 2013
I attached the log-file. Let me know if you need further information about my system. Thank you in advance, Daria
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Daria
We had the same problem on Macs, although they had enough memory. A work around would be to reduce the number of training subjects in the trctrain folder. When we used 26 instead of 33 training subjects, the error disappeared.
Cheers Jürgen
On [DATE], "Antonenko, Daria" <[ADDRESS]> wrote:
Hi Anastasia, my first idea was also that something else might disturb the process, but i replicated the error several times and observed the memory load in the system monitor without running anything else, seemed not memory-intensive at all.. I use a 10 b0 + 64dir DTI sequence, 2.3×2.3×2.3 mm3, TR=7500 ms, TE=86 ms. The preprocessing, dtifit and bedpostx with FSL worked fine.
Daria
Von: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Gesendet: Freitag, 26. April 2013 18:38 An: Antonenko, Daria Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW: [Freesurfer] tracula FS 5.2
Hi Daria - It shouldn't need more than 4Gb based on some quick tests that I ran for this particular step where you're getting the memory error. What are the dimensions of your DWI series? Were you running anything else at the same time that was memory-intensive?
a.y
On Thu, 11 Apr 2013, Antonenko, Daria wrote:
Hi Anastasia, I'm running tracula on linux ubuntu (mint 14) on a lenovo thinkpad edge. it has 8gb ram and 4 CPUs, i think it's a lot.. I did not run tracula before on this computer.
Daria
Daria Antonenko, Dipl.-Psych. Charité - Universitätsmedizin Berlin NeuroCure Clinical Research Center NCRC AG Flöel Charitéplatz 1, 10117 Berlin Tel.: +49 30 450 560 223 Fax: +49 30 450 539 921 E-Mail: daria.antonenko@charite.de
-----Ursprüngliche Nachricht----- Von: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 10. April 2013 17:03 An: Antonenko, Daria Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] tracula FS 5.2
Hi Daria - How much memory does your system have? Were you ever able to run trac-all from the 5.1 version on the same system?
a.y
On Wed, 10 Apr 2013, Antonenko, Daria wrote:
Hi FS experts, I tried to run Tracula with the new FS 5.2 release and came across memory allocation problems in the preprocessing step and would appreciate some advice on solving them:
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice Cannot allocate memory Linux daria-Think 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 i686 i686 i686 GNU/Linux trac-preproc exited with ERRORS at Tue Apr 9 22:21:43 CEST 2013
I attached the log-file. Let me know if you need further information about my system. Thank you in advance, Daria
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------
FYI: In the -prep and -path sections I can run a 77 direction DWI on 33 training subjects with 8Gb RAM, Ubuntu 12.04 but it spills over into the swap memory. The -bedp section is not a memory hog at all.
Cheers,
Sean
On 3/05/13 4:51 PM, "Jürgen Hänggi" j.haenggi@psychologie.uzh.ch wrote:
Hi Daria
We had the same problem on Macs, although they had enough memory. A work around would be to reduce the number of training subjects in the trctrain folder. When we used 26 instead of 33 training subjects, the error disappeared.
Cheers Jürgen
On [DATE], "Antonenko, Daria" <[ADDRESS]> wrote:
Hi Anastasia, my first idea was also that something else might disturb the process, but i replicated the error several times and observed the memory load in the system monitor without running anything else, seemed not memory-intensive at all.. I use a 10 b0 + 64dir DTI sequence, 2.3×2.3×2.3 mm3, TR=7500 ms, TE=86 ms. The preprocessing, dtifit and bedpostx with FSL worked fine.
Daria
Von: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Gesendet: Freitag, 26. April 2013 18:38 An: Antonenko, Daria Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW: [Freesurfer] tracula FS 5.2
Hi Daria - It shouldn't need more than 4Gb based on some quick tests that I ran for this particular step where you're getting the memory error. What are the dimensions of your DWI series? Were you running anything else at the same time that was memory-intensive?
a.y
On Thu, 11 Apr 2013, Antonenko, Daria wrote:
Hi Anastasia, I'm running tracula on linux ubuntu (mint 14) on a lenovo thinkpad edge. it has 8gb ram and 4 CPUs, i think it's a lot.. I did not run tracula before on this computer.
Daria
Daria Antonenko, Dipl.-Psych. Charité - Universitätsmedizin Berlin NeuroCure Clinical Research Center NCRC AG Flöel Charitéplatz 1, 10117 Berlin Tel.: +49 30 450 560 223 Fax: +49 30 450 539 921 E-Mail: daria.antonenko@charite.de
-----Ursprüngliche Nachricht----- Von: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 10. April 2013 17:03 An: Antonenko, Daria Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] tracula FS 5.2
Hi Daria - How much memory does your system have? Were you ever able to run trac-all from the 5.1 version on the same system?
a.y
On Wed, 10 Apr 2013, Antonenko, Daria wrote:
Hi FS experts, I tried to run Tracula with the new FS 5.2 release and came across memory allocation problems in the preprocessing step and would appreciate some advice on solving them:
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice Cannot allocate memory Linux daria-Think 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 i686 i686 i686 GNU/Linux trac-preproc exited with ERRORS at Tue Apr 9 22:21:43 CEST 2013
I attached the log-file. Let me know if you need further information about my system. Thank you in advance, Daria
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
--
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Anastasia Yendiki -
Antonenko, Daria -
Jürgen Hänggi -
Sean Hatton