[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., 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: mkbrainmask not finding fslmaths
Perhaps I should have asked: Do I need to separately install FSL? Thanks > Hi, > > I ran the following preproc-sess command and mkbrainmask-sess failed, with > an error message of not finding fsmaths. I don't know where to be looking > for this file and what previous command should have generated it. Can > anyone help me out? > > Thanks! > Dahlia. > > I ran: > preproc-sess -sf sessid_subj31.txt -df sesspar -fwhm 5 > > The error message was: > ERROR: cannot find either fslmaths for avwmaths > ERROR: mkbrainmask failed > ERROR: mkbrainmask-sess failed > > > mkbrainmask-sess.log says: > mkbrainmask-sess > $Id: mkbrainmask-sess,v 1.12.2.1 2008/10/02 21:56:15 greve Exp $ > Linux mbc.stanford.edu 2.6.22.9-61.fc6 #1 SMP Thu Sep 27 18:07:59 EDT 2007 > x86_64 x86_64 x86_64 GNU/Linux > Tue Jun 30 11:01:46 PDT 2009 > /home/dahlia.sharon/functionals/fba_study_mtloc > -maskstem brain -fsd bold -s mtloc_19may07 -d > /home/dahlia.sharon/functionals/subj31 -update > > This is the command preproc-sess invoked: > mkbrainmask -i 025/f.bhdr -o masks/brain.nii -thresh 0.1 -ndil 1 -nerode 0 > > The data is not on the network so I can't give paths. > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] MNI/Startup.PM error in FreeSurfer 4.4.0
Hello. I just installed FreeSurfer v4.4.0, following all the directions to the letter. When I run recon-all -i -s -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? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer dice coefficient calculation
Hi Jared, yes, the talairach.m3z is the intersubject registration we use for generating the aseg, and you could use it to compute a dice. cheers Bruce On Tue, 30 Jun 2009, Jared Price wrote: 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 ___ 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] mkbrainmask not finding fslmaths
Hi, I ran the following preproc-sess command and mkbrainmask-sess failed, with an error message of not finding fsmaths. I don't know where to be looking for this file and what previous command should have generated it. Can anyone help me out? Thanks! Dahlia. I ran: preproc-sess -sf sessid_subj31.txt -df sesspar -fwhm 5 The error message was: ERROR: cannot find either fslmaths for avwmaths ERROR: mkbrainmask failed ERROR: mkbrainmask-sess failed mkbrainmask-sess.log says: mkbrainmask-sess $Id: mkbrainmask-sess,v 1.12.2.1 2008/10/02 21:56:15 greve Exp $ Linux mbc.stanford.edu 2.6.22.9-61.fc6 #1 SMP Thu Sep 27 18:07:59 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux Tue Jun 30 11:01:46 PDT 2009 /home/dahlia.sharon/functionals/fba_study_mtloc -maskstem brain -fsd bold -s mtloc_19may07 -d /home/dahlia.sharon/functionals/subj31 -update This is the command preproc-sess invoked: mkbrainmask -i 025/f.bhdr -o masks/brain.nii -thresh 0.1 -ndil 1 -nerode 0 The data is not on the network so I can't give paths. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer dice coefficient calculation
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] talairach error during recon-all
Hi Avi, do you have any advise for Dana? thanks Bruce On Tue, 30 Jun 2009, Dana W. Moore wrote: Doug Yes, there is an error message in the talairach_avi.log--I am not sure what it means. The end of the log gives me this message: Dana imgrege: no voxels in register 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 At 06:34 PM 6/29/2009, Douglas N Greve wrote: The error msg asks you to look at transforms/talairach_avi.log. Have you and does it reveal anything? doug Dana W. Moore wrote: 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: dwm2...@med.cornell.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 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: dwm2...@med.cornell.edu ___ 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
Re: [Freesurfer] talairach error during recon-all
Doug Yes, there is an error message in the talairach_avi.log--I am not sure what it means. The end of the log gives me this message: Dana imgrege: no voxels in register 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 At 06:34 PM 6/29/2009, Douglas N Greve wrote: The error msg asks you to look at transforms/talairach_avi.log. Have you and does it reveal anything? doug Dana W. Moore wrote: 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: dwm2...@med.cornell.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 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: dwm2...@med.cornell.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_surf2surf
Hi Jidan, The surface in the native space is given by ?h.white. ?h.sphere and ?h.sphere.reg provide the "mapping" of those vertices of to a spherical representation, and registered spherical representation, respectively. There are ways to get at the Jacobian of these transformations if that is what you are interested in. cheers, Mike H. On Tue, 2009-06-30 at 10:00 +0800, Zhong Jidan wrote: > 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 > ___ > 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
Re: [Freesurfer] autorecon1 error
Hi Fatima, can you send us the recon-all.log? thanks Bruce On Tue, 30 Jun 2009, Ahmed, F, Me wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] image matrix
Hi Feng-Xian,
the surfaces all live in the surf subdirectory. To see how many vertices a
surface contains you can run either mris_euler_numer of mris_info. The
thickness is in the ?h.thickness ("curv" format file - one scalar per
vertex) and the inflated is in ?h.inflated surface format. You can
visualize the thickness in tksurfer by loading the inflated surface then
loading the thickness from the file menu using the load curvature option.
cheers
Bruce
On Tue, 30 Jun 2009, Feng-Xian wrote:
Hi,
I want to check the image matrix after doing autorecon-all. When I look
at the text, I see that ÿÿOriginal Data has (1, 1, 1) mm size and (224, 256,
160) voxels. Data is conformed to 1 mm size and 256 voxels for all
directionsÿÿ. This is said that that image matrix is 256 x 256 x 256. Right?
And, I want to know how many voxels do an inflated surface have? Where
dir and what text do I to get that?
And, do FreeSurfer have a text that including the value of cortical
thickness? I want to know the information of cortical thicknessÿÿs value at
all pixels of whole brain for each subject. If yes, what text has the
information of the value of cortical thickness and where do I find that
text? If no, how can I get the information?
Thank you in advance!
Feng-Xian
-
Chang Gung University Mail Server Web Mail system
By Chang-Gung University Information Center
(http://www.cgu.edu.tw/ic/)
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Re: [Freesurfer] recon-all error
how much ram do you have on your machine? On Tue, 30 Jun 2009 whb...@mail.ustc.edu.cn wrote: 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 ___ 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] autorecon1 error
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 autorecon1_Bert_errors.docx Description: autorecon1_Bert_errors.docx ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] image matrix
Hi, I want to check the image matrix after doing autorecon-all. When I look at the text, I see that “Original Data has (1, 1, 1) mm size and (224, 256, 160) voxels. Data is conformed to 1 mm size and 256 voxels for all directions”. This is said that that image matrix is 256 x 256 x 256. Right? And, I want to know how many voxels do an inflated surface have? Where dir and what text do I to get that? And, do FreeSurfer have a text that including the value of cortical thickness? I want to know the information of cortical thickness’s value at all pixels of whole brain for each subject. If yes, what text has the information of the value of cortical thickness and where do I find that text? If no, how can I get the information? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all error
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
