Freesurfer

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Cannot allocate memory / can't allocate region
by Jürgen Hänggi 01 Jul '09

01 Jul '09

Dear FS experts I am using high resolution (0.75x0.75x0.75 mm) data within FS but the following error occurred: ....... vertex spacing 0.69 +- 0.21 (0.00-->6.06) (max @ vno 265258 --> 114262) face area 0.19 +- 0.10 (0.00-->4.49) mris_make_surfaces(49536) malloc: *** mmap(size=1355776) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(937, 361, 612): could not allocate 1353028 bytes for 356th slice 000: dt: 0.0000, sse=4822516.5, rms=2.25 rms = 2.94, time step reduction 1 of 3 to 0.250... 043: dt: 0.2500, sse=4898456.5, rms=1.89 rms = 1.86, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=5293477.5, rms=1.86 045: dt: 0.1250, sse=5277681.5, rms=1.76 046: dt: 0.1250, sse=5237215.5, rms=1.70 rms = 1.69, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=5270459.0, rms=1.69 positioning took 16.1 minutes inhibiting deformation at non-cortical midline structures... correcting aseg with surfaces... Cannot allocate memory Darwin juergen-haenggis-mac-pro.local 9.7.0 Darwin Kernel Version 9.7.0: Tue Mar 31 22:52:17 PDT 2009; root:xnu-1228.12.14~1/RELEASE_I386 i386 recon-all exited with ERRORS at Wed Jul 1 04:20:34 CEST 2009 [juergen-haenggis-mac-pro:subjects/roman_p_highres_div100/mri] I am using FS 4.4, Mac OSX 10.5, 8 GB RAM, memoryuse unlimited, descriptors 8192 The process terminated before all RAM is active and no swap is used. Any idea? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) 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. ----------------------------------------------------------------------------

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RES: [Freesurfer] Cannot allocate memory / can't allocate region
by ppj＠netfilter.com.br 01 Jul '09

01 Jul '09

Check ulimit -m That's the max mem per process. ulimit -m 0 Maybe will help. -- Pedro Paulo Jr E71 Nokia -----Msg original----- De: Jürgen Hänggi Enviada: 01/07/2009 02:36:36 Para: Freesurfer Mailinglist Assunto: [Freesurfer] Cannot allocate memory / can't allocate region Dear FS experts I am using high resolution (0.75x0.75x0.75 mm) data within FS but the following error occurred: ....... vertex spacing 0.69 +- 0.21 (0.00-->6.06) (max @ vno 265258 --> 114262) face area 0.19 +- 0.10 (0.00-->4.49) mris_make_surfaces(49536) malloc: *** mmap(size=1355776) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(937, 361, 612): could not allocate 1353028 bytes for 356th slice 000: dt: 0.0000, sse=4822516.5, rms=2.25 rms = 2.94, time step reduction 1 of 3 to 0.250... 043: dt: 0.2500, sse=4898456.5, rms=1.89 rms = 1.86, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=5293477.5, rms=1.86 045: dt: 0.1250, sse=5277681.5, rms=1.76 046: dt: 0.1250, sse=5237215.5, rms=1.70 rms = 1.69, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=5270459.0, rms=1.69 positioning took 16.1 minutes inhibiting deformation at non-cortical midline structures... correcting aseg with surfaces... Cannot allocate memory Darwin juergen-haenggis-mac-pro.local 9.7.0 Darwin Kernel Version 9.7.0: Tue Mar 31 22:52:17 PDT 2009; root:xnu-1228.12.14~1/RELEASE_I386 i386 recon-all exited with ERRORS at Wed Jul 1 04:20:34 CEST 2009 [juergen-haenggis-mac-pro:subjects/roman_p_highres_div100/mri] I am using FS 4.4, Mac OSX 10.5, 8 GB RAM, memoryuse unlimited, descriptors 8192 The process terminated before all RAM is active and no swap is used. Any idea? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) 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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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MNI/Startup.PM error in FreeSurfer 4.4.0
by Matthew Koh 30 Jun '09

30 Jun '09

Hello. I just installed FreeSurfer v4.4.0, following all the directions to the letter. When I run recon-all -i <input-file> -s <subject> -autorecon1, I get the following error: Can't locate MNI/Startup.pm in @INC (@INC contains: /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Applications/freesurfer/mni/bin/nu_correct line 37. If it matters, the value of $PERL5LIB is: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 and I'm working in OS X 10.4.11 on a PowerPC. Anyone have any ideas?

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freesurfer dice coefficient calculation
by Jared Price 30 Jun '09

30 Jun '09

Hi freesurfer masters, Quick question on the way freesurfer calculates the dice coefficient. I am interested in getting an INTERsubject dice coefficient as a measure of similarity between 2 subjects. My question is, do I need to do an INTERsubject registration step before calculating the dice in freesurfer? In other words, does freesurfer do any kind of INTERsubject registration at the level of the aseg.mgz file? If it does not, when it calculates an intersubject dice coefficient, a low result could be due simply to poor alignment between scans and not poor anatomical correlation. If anyone has details please let me know. Cheers, Jared

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talairach error during recon-all
by Dana W. Moore 30 Jun '09

30 Jun '09

Hi all, I get the following error message during recon-all: ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Any idea why this is happening? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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mri_surf2surf
by Zhong Jidan 30 Jun '09

30 Jun '09

Hi Freesurfer Experts, I have a question about the use of mri_surf2surf. Can I use this command to convert the sphere of a surface to its native space? To be specific, we can get a sphere if we do inflation and other steps to the white surface , can we transform the sphere back to the orginal white surface? (if we only have sphere and don't have the white surface this time.) I want to try this because after the sphere registration from the subject to the template, although the deformed sphere has one to one correspondance to the original surface of the subject, its representation in the native space should have changed. I want to see clearly in the native space of the surface to check whether the sulci and gyri moves and to which extent, so I want to know whether the sur2surf command can transform the deformed sphere to its native space. If yes, could you tell me how to use this command, thanks a lot!! -- Regards, Jidan

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autorecon1 error
by Ahmed, F, Me <fahmed＠sun.ac.za> 30 Jun '09

30 Jun '09

Hi, I had problems running autorecon 1 with my own subject group, so I decided to see if I could run the tutorial with Bert. I ran the motion correction, and then tried autorecon 1 and got the following error (please see the attached word document to see my output). ERROR: converting nu to COR/mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue Jun 30 09:43:14 BST 2009 Can anyone please tell me what this means and if I can correct it? Thanks, Fatima

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recon-all error
by whblqh＠mail.ustc.edu.cn 30 Jun '09

30 Jun '09

Hello! I just setup "freesurfer-Linux-centos4-stable-pub-v4.4.0" on linux 2.6.21-1.3194.fc7 . to test freesurfer, I successfully run "recon-all -s bert -autorecon1" and "recon-all -s bert -autorecon3", but "recon-all -s bert -autorecon2", exited with ERRORS,as follows: "writing output transformation to transforms/talairach.m3z... registration took 5 hours, 40 minutes and 53 seconds. #-------------------------------------- #@# CA Reg Inv Tue Jun 30 08:14:28 CST 2009 /home/whb/soft/freesurfer/subjects/bert/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Tue Jun 30 08:16:04 CST 2009 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /home/whb/soft/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/home/whb/soft/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11097896 nonbrain voxels erased writing output to nu_noneck.mgz... mghWrite(nu_noneck.mgz, -1): could not open file ERROR: opening pipe gzip -f -c > nu_noneck.mgz, errno = 12 Cannot allocate memory Linux localhost.localdomain 2.6.21-1.3194.fc7 #1 SMP Wed May 23 22:35:01 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue Jun 30 08:17:59 CST 2009" I don't know what's wrong. would you like to help me? thanks advance! Hai-bao wang

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Re: [Freesurfer] merging 2 .mgz files?
by rudolph＠nmr.mgh.harvard.edu 29 Jun '09

29 Jun '09

$>mris_calc -o combined.mgz vol1.mgz add vol2.mgz (i.e. combined.mgz = vol1.mgz + vol2.mgz) ------Original Message------ From: xforever(a)ucla.edu Sender: freesurfer-bounces(a)nmr.mgh.harvard.edu To: 'Freesurfer Mailing List' Subject: [Freesurfer] merging 2 .mgz files? Sent: Jun 29, 2009 16:57 Dear Freesurfer Experts, I was wondering if its possible to combine 2 mgz files? the 2 files don't have overlaps.. sincerely, Andy _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Sent via BlackBerry from T-Mobile

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RES: Re: [Freesurfer] Where can I read the manual for old freesurfer version (some new information)
by ppj＠netfilter.com.br 29 Jun '09

29 Jun '09

Zhang In the wiki page there's a feature to check the previous version of each page. -- Pedro Paulo Jr E71 Nokia -----Msg original----- De: Bruce Fischl Enviada: 29/06/2009 17:30:10 Para: Zhang, Xiaochu (NIH/NIDA) [F] Cc: 'freesurfer(a)nmr.mgh.harvard.edu' Assunto: Re: [Freesurfer] Where can I read the manual for old freesurfer version (some new information) I'm not sure we have it so easily. Does anyone know? On Mon, 29 Jun 2009, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > The freesurfer I am using now is this version, "freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.4". I knew there is much improved in the current version.However, I have about 80 participants done in this old version. I only want to add several new participants and do some group anlaysis. Today I read the wiki and found a lot of things in "GroupAnalysis" have been changed. I tried to follow the new workflows but I found it is not suit to old verison. Who can do me a favor and give me the manual for the old version? My advisor asked me for result just now. > Thank you so much! > > > > Xiaochu Zhang PhD > Visiting Research Fellow > Neuroimaging Research Branch > National Institute on Drug Abuse - IRP > Biomedical Research Center > 251 Bayview Blvd. > Suite 200 (NIDA) > Baltimore MD > 21224 > Tel: 443-740-2619 > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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