Dear FS experts
I tried to run make_average_subject in the past with 92 subjects and got the following error: Cannot allocate memory. This is now on the to-do list of the FS website. Then I bought some additional RAM and changed from OS X tiger to leopard. Now I tried it again and get this error:
[Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit descriptors 4096 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 4096 memorylocked unlimited maxproc 266 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% make_average_subject --subjects SNPs_Vp* limit: descriptors: Can't remove limit (Invalid argument) [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi%
I set the descriptor limit to 4096, but the make_average_subject command will not start anymore.
Any idea what is wrong here?
Thanks in advance Best regards Juergen
----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------
Juergen,
Edit the 'make_average_subject' script removing (or commenting-out) the line 'limit descriptors unlimited'. You may have to do the same for 'make_average_surface' and 'make_average_volume'. Although in v4.0, these should already be commented-out.
Nick
On Mon, 2008-01-28 at 16:29 +0100, Juergen Haenggi wrote:
Dear FS experts
I tried to run make_average_subject in the past with 92 subjects and got the following error: Cannot allocate memory. This is now on the to-do list of the FS website. Then I bought some additional RAM and changed from OS X tiger to leopard. Now I tried it again and get this error:
[Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit descriptors 4096 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 4096 memorylocked unlimited maxproc 266 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% make_average_subject --subjects SNPs_Vp* limit: descriptors: Can't remove limit (Invalid argument) [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi%
I set the descriptor limit to 4096, but the make_average_subject command will not start anymore.
Any idea what is wrong here?
Thanks in advance Best regards Juergen
Juergen Haenggi Ph.D. (Dr. des.) Division of 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@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi James,
thanks for the careful analysis. Not sure why it's not using swap, but we'll get back to you soon.
have a good weekend, Bruce
On Sat, 2 Feb 2008, James N. Porter wrote:
So, I believe I have isolated the problem. The failure happens during the mri_concat phase of make_average_volumes. The seg-subj#.mgh temp files that are being concatenated are 65 MB each and I can successfully run 59 subjects, but for 60 subjects and up, mri_concat exits immediately with the error message as written below. I have 4GB of memory, and 65*59 is less than 4 GB so that works; add any more subjects and the process is shut down. It appears that mri_concat checks to see how much memory will be needed to hold all those .mgh files in active use, then checks the machine to see how much physical memory is available. I can easily set up a larger swap file to handle the full 175*65 that is needed (it will be insanely slow, but that's better than nothing). However, I can't get FreeSurfer to utilize the swap space I already have available.
I watched the whole make_average_volumes process play out on my resource monitor (I imagine that's what watching NASCAR is like--Come on, just crash already!) and while it came very close to using all 4GB--leaving a paltry 19 MB free at most points--it didn't touch the swap at any point during the run. This is not the case with Matlab and other programs, which will greedily eat up physical memory then seek out the swap. While I appreciate that the FreeSurfer programs are set up to be judicious consumers of resources, is there some sort of environmental variable in FreeSurfer or line of code in mri_concat that I can modify that would allow the programs to reach out and use the swap space?
Thanks, Jim
Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota
James N. Porter wrote: Juergen--Have you had successful resolution to this problem?
Nick--I'm attempting to average 175 subjects, but make_average_volume returns the same error as Juergen reports. > Allocing output > MRIalloc(256,256,256): could not allocate 262144 bytes for 15547th slice I'm running freesurfer-Linux-rh9-stable-pub-v4.0.1 on SUSE Linux 9.3 2.6.11.4-21.17-smp x86_64, with a pair of Pentium 3.20 GHz processors, 4 GB of physical memory and 8 GB of swap memory. My limits are also quite liberal. > cputime unlimited > filesize unlimited > datasize unlimited > stacksize unlimited > coredumpsize 0 kbytes > memoryuse unlimited > vmemoryuse unlimited > descriptors 1024 > memorylocked 32 kbytes > maxproc 28660 I've tried to also use the alternative script posted by Doug Greve (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06641.html). That also returns the same error. Any suggestions? Many thanks,
Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota
Nick Schmansky wrote:Juergen,
Edit the 'make_average_subject' script removing (or commenting-out) the line 'limit descriptors unlimited'. You may have to do the same for 'make_average_surface' and 'make_average_volume'. Although in v4.0, these should already be commented-out.
Nick
On Mon, 2008-01-28 at 16:29 +0100, Juergen Haenggi wrote:
Dear FS experts
I tried to run make_average_subject in the past with 92 subjects and got the following error: Cannot allocate memory. This is now on the to-do list of the FS website. Then I bought some additional RAM and changed from OS X tiger to leopard. Now I tried it again and get this error:
[Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit descriptors 4096 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 4096 memorylocked unlimited maxproc 266 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% make_average_subject --subjects SNPs_Vp* limit: descriptors: Can't remove limit (Invalid argument) [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi%
I set the descriptor limit to 4096, but the make_average_subject command will not start anymore.
Any idea what is wrong here?
Thanks in advance Best regards Juergen
Juergen Haenggi Ph.D. (Dr. des.) Division of 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@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi James, hi Bruce
Thanks a lot for your help. I can confirm that make_average_subject did not used any swap memory in my case too when I tried to average 92 subjects with 5 GB RAM. Meanwhile I have 8 GB RAM and the process stopped before all 8 GB RAM are active.
Regards Juergen
On 2.2.2008 19:09 Uhr, "James N. Porter" porterj@umn.edu wrote:
So, I believe I have isolated the problem. The failure happens during the mri_concat phase of make_average_volumes. The seg-subj#.mgh temp files that are being concatenated are 65 MB each and I can successfully run 59 subjects, but for 60 subjects and up, mri_concat exits immediately with the error message as written below. I have 4GB of memory, and 65*59 is less than 4 GB so that works; add any more subjects and the process is shut down. It appears that mri_concat checks to see how much memory will be needed to hold all those .mgh files in active use, then checks the machine to see how much physical memory is available. I can easily set up a larger swap file to handle the full 175*65 that is needed (it will be insanely slow, but that's better than nothing). However, I can't get FreeSurfer to utilize the swap space I already have available.
I watched the whole make_average_volumes process play out on my resource monitor (I imagine that's what watching NASCAR is like--Come on, just crash already!) and while it came very close to using all 4GB--leaving a paltry 19 MB free at most points--it didn't touch the swap at any point during the run. This is not the case with Matlab and other programs, which will greedily eat up physical memory then seek out the swap. While I appreciate that the FreeSurfer programs are set up to be judicious consumers of resources, is there some sort of environmental variable in FreeSurfer or line of code in mri_concat that I can modify that would allow the programs to reach out and use the swap space?
Thanks, Jim
Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota
James N. Porter wrote:
Juergen--Have you had successful resolution to this problem?
Nick--I'm attempting to average 175 subjects, but make_average_volume returns the same error as Juergen reports.
> Allocing output > MRIalloc(256,256,256): could not allocate 262144 bytes for 15547th
slice
I'm running freesurfer-Linux-rh9-stable-pub-v4.0.1 on SUSE Linux 9.3 2.6.11.4-21.17-smp x86_64, with a pair of Pentium 3.20 GHz processors, 4 GB of physical memory and 8 GB of swap memory. My limits are also quite liberal.
> cputime unlimited > filesize unlimited > datasize unlimited > stacksize unlimited > coredumpsize 0 kbytes > memoryuse unlimited > vmemoryuse unlimited > descriptors 1024 > memorylocked 32 kbytes > maxproc 28660I've tried to also use the alternative script posted by Doug Greve (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06641.html). That also returns the same error.
Any suggestions?
Many thanks,
Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota
Nick Schmansky wrote:
Juergen,
Edit the 'make_average_subject' script removing (or commenting-out) the line 'limit descriptors unlimited'. You may have to do the same for 'make_average_surface' and 'make_average_volume'. Although in v4.0, these should already be commented-out.
Nick
On Mon, 2008-01-28 at 16:29 +0100, Juergen Haenggi wrote:
Dear FS experts
I tried to run make_average_subject in the past with 92 subjects and got the following error: Cannot allocate memory. This is now on the to-do list of the FS website. Then I bought some additional RAM and changed from OS X tiger to leopard. Now I tried it again and get this error:
[Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit descriptors 4096 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 4096 memorylocked unlimited maxproc 266 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% make_average_subject --subjects SNPs_Vp* limit: descriptors: Can't remove limit (Invalid argument) [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi%
I set the descriptor limit to 4096, but the make_average_subject command will not start anymore.
Any idea what is wrong here?
Thanks in advance Best regards Juergen
Juergen Haenggi Ph.D. (Dr. des.) Division of 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@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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
----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------
I think the failure happens when it tries to create the group aseg.mgz. I changed the code on 1/3/08 so that it would just print a warning and continue, but I don't think this version is being distributed yet.
I've put new versions of make_average_subject make_average_surface make_average_volume
here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve
Copy them into $FREESURFER_HOME/bin (make backups:), and give it a try.
doug
James N. Porter wrote:
So, I believe I have isolated the problem. The failure happens during the mri_concat phase of make_average_volumes. The seg-subj#.mgh temp files that are being concatenated are 65 MB each and I can successfully run 59 subjects, but for 60 subjects and up, mri_concat exits immediately with the error message as written below. I have 4GB of memory, and 65*59 is less than 4 GB so that works; add any more subjects and the process is shut down. It appears that mri_concat checks to see how much memory will be needed to hold all those .mgh files in active use, then checks the machine to see how much physical memory is available. I can easily set up a larger swap file to handle the full 175*65 that is needed (it will be insanely slow, but that's better than nothing). However, I can't get FreeSurfer to utilize the swap space I already have available.
I watched the whole make_average_volumes process play out on my resource monitor (I imagine that's what watching NASCAR is like--Come on, just crash already!) and while it came very close to using all 4GB--leaving a paltry 19 MB free at most points--it didn't touch the swap at any point during the run. This is not the case with Matlab and other programs, which will greedily eat up physical memory then seek out the swap. While I appreciate that the FreeSurfer programs are set up to be judicious consumers of resources, is there some sort of environmental variable in FreeSurfer or line of code in mri_concat that I can modify that would allow the programs to reach out and use the swap space?
Thanks, Jim
Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota
James N. Porter wrote:
Juergen--Have you had successful resolution to this problem?
Nick--I'm attempting to average 175 subjects, but make_average_volume returns the same error as Juergen reports. > Allocing output > MRIalloc(256,256,256): could not allocate 262144 bytes for 15547th slice
I'm running freesurfer-Linux-rh9-stable-pub-v4.0.1 on SUSE Linux 9.3 2.6.11.4-21.17-smp x86_64, with a pair of Pentium 3.20 GHz processors, 4 GB of physical memory and 8 GB of swap memory. My limits are also quite liberal. > cputime unlimited > filesize unlimited > datasize unlimited > stacksize unlimited > coredumpsize 0 kbytes > memoryuse unlimited > vmemoryuse unlimited > descriptors 1024 > memorylocked 32 kbytes > maxproc 28660
I've tried to also use the alternative script posted by Doug Greve (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06641.html). That also returns the same error.
Any suggestions?
Many thanks,
Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota
Nick Schmansky wrote:
Juergen,
Edit the 'make_average_subject' script removing (or commenting-out) the line 'limit descriptors unlimited'. You may have to do the same for 'make_average_surface' and 'make_average_volume'. Although in v4.0, these should already be commented-out.
Nick
On Mon, 2008-01-28 at 16:29 +0100, Juergen Haenggi wrote:
Dear FS experts
I tried to run make_average_subject in the past with 92 subjects and got the following error: Cannot allocate memory. This is now on the to-do list of the FS website. Then I bought some additional RAM and changed from OS X tiger to leopard. Now I tried it again and get this error:
[Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit descriptors 4096 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 4096 memorylocked unlimited maxproc 266 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% make_average_subject --subjects SNPs_Vp* limit: descriptors: Can't remove limit (Invalid argument) [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi%
I set the descriptor limit to 4096, but the make_average_subject command will not start anymore.
Any idea what is wrong here?
Thanks in advance Best regards Juergen
Juergen Haenggi Ph.D. (Dr. des.) Division of 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@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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
Hi Doug
Thanks a lot for the new version of the make_average_subject scripts. I tried it but the following error occurred:
Reading surface /Applications/freesurfer/subjects/average/surf/rh.white Loading annotations from /Applications/freesurfer/subjects/average/label/rh.aparc.a2005s.annot max index = 81 3 387 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_c ingulate-Isthmus.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_c ingulate-Isthmus.label 4 2350 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_c ingulate-Main_part.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_c ingulate-Main_part.label 5 1412 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_c uneus.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_c uneus.label 6 1479 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_f rontal_inf-Opercular_part.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_f rontal_inf-Opercular_part.label . . . . . LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_s uborbital.label 77 1999 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_s ubparietal.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_s ubparietal.label 79 1276 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_t emporal_inferior.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_t emporal_inferior.label 80 7673 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_t emporal_superior.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_t emporal_superior.label 81 365 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_t emporal_transverse.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_t emporal_transverse.label mri_mergelabels -o /Applications/freesurfer/subjects/average/label/rh.cortex.label -d /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236 Done /Applications/freesurfer/subjects/average/surf mris_preproc --out rh.orig.avg.area.mgh --f /tmp/subjlist.69236 --target average --hemi rh --area orig --mean --srcsurfreg sphere.reg ERROR: flag --srcsurfreg not recognized [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi%
It seems that there is a index maximum of 81 and therefore the flag --srcsurfreg is not recognized.
Thanks Regards Juergen
On 6.2.2008 23:05 Uhr, "Doug Greve" greve@nmr.mgh.harvard.edu wrote:
I think the failure happens when it tries to create the group aseg.mgz. I changed the code on 1/3/08 so that it would just print a warning and continue, but I don't think this version is being distributed yet.
I've put new versions of make_average_subject make_average_surface make_average_volume
here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve
Copy them into $FREESURFER_HOME/bin (make backups:), and give it a try.
doug
James N. Porter wrote:
So, I believe I have isolated the problem. The failure happens during the mri_concat phase of make_average_volumes. The seg-subj#.mgh temp files that are being concatenated are 65 MB each and I can successfully run 59 subjects, but for 60 subjects and up, mri_concat exits immediately with the error message as written below. I have 4GB of memory, and 65*59 is less than 4 GB so that works; add any more subjects and the process is shut down. It appears that mri_concat checks to see how much memory will be needed to hold all those .mgh files in active use, then checks the machine to see how much physical memory is available. I can easily set up a larger swap file to handle the full 175*65 that is needed (it will be insanely slow, but that's better than nothing). However, I can't get FreeSurfer to utilize the swap space I already have available.
I watched the whole make_average_volumes process play out on my resource monitor (I imagine that's what watching NASCAR is like--Come on, just crash already!) and while it came very close to using all 4GB--leaving a paltry 19 MB free at most points--it didn't touch the swap at any point during the run. This is not the case with Matlab and other programs, which will greedily eat up physical memory then seek out the swap. While I appreciate that the FreeSurfer programs are set up to be judicious consumers of resources, is there some sort of environmental variable in FreeSurfer or line of code in mri_concat that I can modify that would allow the programs to reach out and use the swap space?
Thanks, Jim
Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota
James N. Porter wrote:
Juergen--Have you had successful resolution to this problem?
Nick--I'm attempting to average 175 subjects, but make_average_volume returns the same error as Juergen reports.
> Allocing output > MRIalloc(256,256,256): could not allocate 262144 bytes for 15547th
slice
I'm running freesurfer-Linux-rh9-stable-pub-v4.0.1 on SUSE Linux 9.3 2.6.11.4-21.17-smp x86_64, with a pair of Pentium 3.20 GHz processors, 4 GB of physical memory and 8 GB of swap memory. My limits are also quite liberal.
> cputime unlimited > filesize unlimited > datasize unlimited > stacksize unlimited > coredumpsize 0 kbytes > memoryuse unlimited > vmemoryuse unlimited > descriptors 1024 > memorylocked 32 kbytes > maxproc 28660I've tried to also use the alternative script posted by Doug Greve (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06641.html). That also returns the same error.
Any suggestions?
Many thanks,
Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota
Nick Schmansky wrote:
Juergen,
Edit the 'make_average_subject' script removing (or commenting-out) the line 'limit descriptors unlimited'. You may have to do the same for 'make_average_surface' and 'make_average_volume'. Although in v4.0, these should already be commented-out.
Nick
On Mon, 2008-01-28 at 16:29 +0100, Juergen Haenggi wrote:
Dear FS experts
I tried to run make_average_subject in the past with 92 subjects and got the following error: Cannot allocate memory. This is now on the to-do list of the FS website. Then I bought some additional RAM and changed from OS X tiger to leopard. Now I tried it again and get this error:
[Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit descriptors 4096 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 4096 memorylocked unlimited maxproc 266 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% make_average_subject --subjects SNPs_Vp* limit: descriptors: Can't remove limit (Invalid argument) [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi%
I set the descriptor limit to 4096, but the make_average_subject command will not start anymore.
Any idea what is wrong here?
Thanks in advance Best regards Juergen
Juergen Haenggi Ph.D. (Dr. des.) Division of 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@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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
----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------
The problem is that it is calling mris_preproc with --srcsurfreg, and you do not have the version of mris_preproc that accepts this flag. You can edit it to make it --surfreg. Or, you can get a new copy of make_average_surface from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
doug
Juergen Haenggi wrote:
Hi Doug
Thanks a lot for the new version of the make_average_subject scripts. I tried it but the following error occurred:
Reading surface /Applications/freesurfer/subjects/average/surf/rh.white Loading annotations from /Applications/freesurfer/subjects/average/label/rh.aparc.a2005s.annot max index = 81 3 387 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_cingulate-Isthmus.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_cingulate-Isthmus.label 4 2350 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_cingulate-Main_part.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_cingulate-Main_part.label 5 1412 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_cuneus.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_cuneus.label 6 1479 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_frontal_inf-Opercular_part.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_frontal_inf-Opercular_part.label . . . . . LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_suborbital.label 77 1999 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_subparietal.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_subparietal.label 79 1276 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_temporal_inferior.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_temporal_inferior.label 80 7673 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_temporal_superior.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_temporal_superior.label 81 365 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_temporal_transverse.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_temporal_transverse.label mri_mergelabels -o /Applications/freesurfer/subjects/average/label/rh.cortex.label -d /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236 Done /Applications/freesurfer/subjects/average/surf mris_preproc --out rh.orig.avg.area.mgh --f /tmp/subjlist.69236 --target average --hemi rh --area orig --mean --srcsurfreg sphere.reg ERROR: flag --srcsurfreg not recognized [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi%
It seems that there is a index maximum of 81 and therefore the flag --srcsurfreg is not recognized.
Thanks Regards Juergen
On 6.2.2008 23:05 Uhr, "Doug Greve" greve@nmr.mgh.harvard.edu wrote:
I think the failure happens when it tries to create the group aseg.mgz. I changed the code on 1/3/08 so that it would just print a warning and continue, but I don't think this version is being distributed yet. I've put new versions of make_average_subject make_average_surface make_average_volume here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve Copy them into $FREESURFER_HOME/bin (make backups:), and give it a try. doug James N. Porter wrote: So, I believe I have isolated the problem. The failure happens during the mri_concat phase of make_average_volumes. The seg-subj#.mgh temp files that are being concatenated are 65 MB each and I can successfully run 59 subjects, but for 60 subjects and up, mri_concat exits immediately with the error message as written below. I have 4GB of memory, and 65*59 is less than 4 GB so that works; add any more subjects and the process is shut down. It appears that mri_concat checks to see how much memory will be needed to hold all those .mgh files in active use, then checks the machine to see how much physical memory is available. I can easily set up a larger swap file to handle the full 175*65 that is needed (it will be insanely slow, but that's better than nothing). However, I can't get FreeSurfer to utilize the swap space I already have available. I watched the whole make_average_volumes process play out on my resource monitor (I imagine that's what watching NASCAR is like--Come on, just crash already!) and while it came very close to using all 4GB--leaving a paltry 19 MB free at most points--it didn't touch the swap at any point during the run. This is not the case with Matlab and other programs, which will greedily eat up physical memory then seek out the swap. While I appreciate that the FreeSurfer programs are set up to be judicious consumers of resources, is there some sort of environmental variable in FreeSurfer or line of code in mri_concat that I can modify that would allow the programs to reach out and use the swap space? Thanks, Jim --------- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota James N. Porter wrote: Juergen--Have you had successful resolution to this problem? Nick--I'm attempting to average 175 subjects, but make_average_volume returns the same error as Juergen reports. > Allocing output > MRIalloc(256,256,256): could not allocate 262144 bytes for 15547th slice I'm running freesurfer-Linux-rh9-stable-pub-v4.0.1 on SUSE Linux 9.3 2.6.11.4-21.17-smp x86_64, with a pair of Pentium 3.20 GHz processors, 4 GB of physical memory and 8 GB of swap memory. My limits are also quite liberal. > cputime unlimited > filesize unlimited > datasize unlimited > stacksize unlimited > coredumpsize 0 kbytes > memoryuse unlimited > vmemoryuse unlimited > descriptors 1024 > memorylocked 32 kbytes > maxproc 28660 I've tried to also use the alternative script posted by Doug Greve (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06641.html). <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06641.html%29.> That also returns the same error. Any suggestions? Many thanks, --------- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota Nick Schmansky wrote: Juergen, Edit the 'make_average_subject' script removing (or commenting-out) the line 'limit descriptors unlimited'. You may have to do the same for 'make_average_surface' and 'make_average_volume'. Although in v4.0, these should already be commented-out. Nick On Mon, 2008-01-28 at 16:29 +0100, Juergen Haenggi wrote: Dear FS experts I tried to run make_average_subject in the past with 92 subjects and got the following error: Cannot allocate memory. This is now on the to-do list of the FS website. Then I bought some additional RAM and changed from OS X tiger to leopard. Now I tried it again and get this error: [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit descriptors 4096 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 4096 memorylocked unlimited maxproc 266 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% make_average_subject --subjects SNPs_Vp* limit: descriptors: Can't remove limit (Invalid argument) [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% I set the descriptor limit to 4096, but the make_average_subject command will not start anymore. Any idea what is wrong here? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------- _______________________________________________ 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
Juergen Haenggi Ph.D. (Dr. des.) Division of 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@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
Hi Doug
Thanks for the new version of make_average_surface. I tried it but the old error came back again:
Allocing output mri_concat(28362) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 13930th slice
Cannot allocate memory [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi%
Sorry Regards Juergen
On 11.2.2008 18:52 Uhr, "Doug Greve" greve@nmr.mgh.harvard.edu wrote:
The problem is that it is calling mris_preproc with --srcsurfreg, and you do not have the version of mris_preproc that accepts this flag. You can edit it to make it --surfreg. Or, you can get a new copy of make_average_surface from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_sur face
doug
Juergen Haenggi wrote:
Re: [Freesurfer] Problem make_average_subject Hi Doug
Thanks a lot for the new version of the make_average_subject scripts. I tried it but the following error occurred:
Reading surface /Applications/freesurfer/subjects/average/surf/rh.white Loading annotations from /Applications/freesurfer/subjects/average/label/rh.aparc.a2005s.annot max index = 81 3 387 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_ci ngulate-Isthmus.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_ci ngulate-Isthmus.label 4 2350 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_ci ngulate-Main_part.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_ci ngulate-Main_part.label 5 1412 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_cu neus.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_cu neus.label 6 1479 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_fr ontal_inf-Opercular_part.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_fr ontal_inf-Opercular_part.label . . . . . LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_su borbital.label 77 1999 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_su bparietal.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_su bparietal.label 79 1276 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_te mporal_inferior.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_te mporal_inferior.label 80 7673 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_te mporal_superior.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_te mporal_superior.label 81 365 /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_te mporal_transverse.label LabelWrite: saving to /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_te mporal_transverse.label mri_mergelabels -o /Applications/freesurfer/subjects/average/label/rh.cortex.label -d /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236 Done /Applications/freesurfer/subjects/average/surf mris_preproc --out rh.orig.avg.area.mgh --f /tmp/subjlist.69236 --target average --hemi rh --area orig --mean --srcsurfreg sphere.reg ERROR: flag --srcsurfreg not recognized [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi%
It seems that there is a index maximum of 81 and therefore the flag --srcsurfreg is not recognized.
Thanks Regards Juergen
On 6.2.2008 23:05 Uhr, "Doug Greve" greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu wrote:
I think the failure happens when it tries to create the group aseg.mgz. I changed the code on 1/3/08 so that it would just print a warning and continue, but I don't think this version is being distributed yet.
I've put new versions of make_average_subject make_average_surface make_average_volume
here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve
Copy them into $FREESURFER_HOME/bin (make backups:), and give it a try.
doug
James N. Porter wrote:
So, I believe I have isolated the problem. The failure happens during the mri_concat phase of make_average_volumes. The seg-subj#.mgh temp files that are being concatenated are 65 MB each and I can successfully run 59 subjects, but for 60 subjects and up, mri_concat exits immediately with the error message as written below. I have 4GB of memory, and 65*59 is less than 4 GB so that works; add any more subjects and the process is shut down. It appears that mri_concat checks to see how much memory will be needed to hold all those .mgh files in active use, then checks the machine to see how much physical memory is available. I can easily set up a larger swap file to handle the full 175*65 that is needed (it will be insanely slow, but that's better than nothing). However, I can't get FreeSurfer to utilize the swap space I already have available.
I watched the whole make_average_volumes process play out on my resource monitor (I imagine that's what watching NASCAR is like--Come on, just crash already!) and while it came very close to using all 4GB--leaving a paltry 19 MB free at most points--it didn't touch the swap at any point during the run. This is not the case with Matlab and other programs, which will greedily eat up physical memory then seek out the swap. While I appreciate that the FreeSurfer programs are set up to be judicious consumers of resources, is there some sort of environmental variable in FreeSurfer or line of code in mri_concat that I can modify that would allow the programs to reach out and use the swap space?
Thanks, Jim
Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota
James N. Porter wrote:
Juergen--Have you had successful resolution to this problem?
Nick--I'm attempting to average 175 subjects, but make_average_volume returns the same error as Juergen reports.
> Allocing output > MRIalloc(256,256,256): could not allocate 262144 bytes for 15547th
slice
I'm running freesurfer-Linux-rh9-stable-pub-v4.0.1 on SUSE Linux 9.3 2.6.11.4-21.17-smp x86_64, with a pair of Pentium 3.20 GHz processors, 4 GB of physical memory and 8 GB of swap memory. My limits are also quite liberal.
> cputime unlimited > filesize unlimited > datasize unlimited > stacksize unlimited > coredumpsize 0 kbytes > memoryuse unlimited > vmemoryuse unlimited > descriptors 1024 > memorylocked 32 kbytes > maxproc 28660I've tried to also use the alternative script posted by Doug Greve (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06641.html) . http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06641.html% 29. That also returns the same error.
Any suggestions?
Many thanks,
Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota
Nick Schmansky wrote:
Juergen,
Edit the 'make_average_subject' script removing (or commenting-out) the line 'limit descriptors unlimited'. You may have to do the same for 'make_average_surface' and 'make_average_volume'. Although in v4.0, these should already be commented-out.
Nick
On Mon, 2008-01-28 at 16:29 +0100, Juergen Haenggi wrote:
> > Dear FS experts > > I tried to run make_average_subject in the past with 92 subjects and got > the > following error: Cannot allocate memory. This is now on the to-do list > of > the FS website. Then I bought some additional RAM and changed from OS X > tiger to leopard. Now I tried it again and get this error: > > [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit > descriptors 4096 > [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit > cputime unlimited > filesize unlimited > datasize 6144 kbytes > stacksize 8192 kbytes > coredumpsize 0 kbytes > memoryuse unlimited > descriptors 4096 > memorylocked unlimited > maxproc 266 > [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% > make_average_subject --subjects SNPs_Vp* > limit: descriptors: Can't remove limit (Invalid argument) > [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% > > I set the descriptor limit to 4096, but the make_average_subject command > will not start anymore. > > Any idea what is wrong here? > > Thanks in advance > Best regards > Juergen > > ----------------------------------------------------------- > Juergen Haenggi > Ph.D. (Dr. des.) > Division of 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@psychologie.uzh.ch (email) > http://www.psychologie.uzh.ch/neuropsy/ (website) > http://www.juergenhaenggi.ch (private website) > ----------------------------------------------------------- > > > _______________________________________________ > 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
Juergen Haenggi Ph.D. (Dr. des.) Division of 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@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
James N. Porter -
Juergen Haenggi -
Nick Schmansky