Re: [Freesurfer] how/where is talairach.xfm used?
Hi Mike, it is used a bit in mri_fill I think, although it might actually have been removed now that we use the aseg. There is also the option of using it to initialize the spherical morph, but that is disabled by default, so it's not used very much. Generally as long as it's not dramatically wrong it won't effect the processing, but will of course mean the tal coords you report are wrong. cheers, Bruce On Fri, 12 Oct 2007, Michael Harms wrote: Is talairach.xfm even used as input for any stage of autorecon2 or 3? (Or, is it just the talairach.lta and talairach.m3z files?) thanks, Mike H. On Thu, 2007-10-11 at 16:28 -0400, Doug Greve wrote: It is not that important from a recon standpoint. However, if you intend to report talairach coods, create an average surface, or use that talairach transform in any way, it will be a problem. doug Michael Harms wrote: Hello, We are running FS v3.0.5 on some elderly brains, and the talairach transform (as assessed via tkregister2 with fstal flag) is inaccurate in an appreciable number of the scans we have examined so far. Frequently, the inaccuracies involve primarily scaling or translation, although in one instance the rotation was way-off (such that the cardinal axes were basically swapped). However, even for this worst case, the white and pial surfaces, as well as the aseg, look reasonable. (I haven't run autorecon3 to create the surface parcellations yet). To what extent is talairach.xfm important for the autorecon2 & 3 stages? If surfaces and aseg look ok, can an inaccurate talairach.xfm just be ignored if we are not going to be averaging functional data? Will the surface parcellations perhaps be affected somehow? Looking at ReconAllDevTable it appears that talairach.lta and talairach.m3z are the primary inputs to stages 2 and 3. So, I'm wondering how the .xfm relates to the .lta and .m3z files...? Lastly, the particularly bad .xfm under v3.0.5 looks fine when created using v4.0.1. If we need or want accurate .xfm's would it be appropriate to run autorecon1 under v4 but then switch to v3 for autorecon2 & 3 so as to maintain compatibility with other subjects processed under v3? thanks, Mike H. ___ 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] how/where is talairach.xfm used?
Mike, I think it is perfectly acceptable to use the talairach.xfm file generated for a subject by v4 for use with v3.0.5 processing. There is no difference in the file format, it is just more accurate. Another feature in v4 is a check of the talairach.xfm file against a set of known-good alignments (-tal-check), so if your subjects pass 'recon-all -s -talairach -tal-check' with v4, then you can be assured that the talairach.xfm is as good as you can get. Nick On Fri, 2007-10-12 at 09:30 -0500, Michael Harms wrote: > Yes, based on a small N, version 4 does seem much more robust. > > So, if we wanted accurate .xfm's without requiring manual editing, would > it be appropriate/fair to use v4 for autorecon1, but then use v3.0.5 for > autorecon2 and 3, so as to maintain compatibility with other data > processed under v3? > > thanks, > Mike H. > > On Thu, 2007-10-11 at 17:30 -0400, Bruce Fischl wrote: > > it's also worth noting that version 4 comes with Avi Snyder's most > > excellent talairaching instead of the one we used to use, which in our > > experience is *extremely* accurate and Robust (thanks Avi!). > > > > Bruce > > > > On Thu, 11 Oct > > 2007, Doug Greve wrote: > > > > > It is not that important from a recon standpoint. However, if you intend > > > to > > > report talairach coods, create an average surface, or use that talairach > > > transform in any way, it will be a problem. > > > > > > doug > > > > > > Michael Harms wrote: > > > > > >> Hello, > > >> We are running FS v3.0.5 on some elderly brains, and the talairach > > >> transform (as assessed via tkregister2 with fstal flag) is inaccurate in > > >> an appreciable number of the scans we have examined so far. Frequently, > > >> the inaccuracies involve primarily scaling or translation, although in > > >> one instance the rotation was way-off (such that the cardinal axes were > > >> basically swapped). However, even for this worst case, the white and > > >> pial surfaces, as well as the aseg, look reasonable. (I haven't run > > >> autorecon3 to create the surface parcellations yet). > > >> > > >> To what extent is talairach.xfm important for the autorecon2 & 3 stages? > > >> If surfaces and aseg look ok, can an inaccurate talairach.xfm just be > > >> ignored if we are not going to be averaging functional data? Will the > > >> surface parcellations perhaps be affected somehow? > > >> > > >> Looking at ReconAllDevTable it appears that talairach.lta and > > >> talairach.m3z are the primary inputs to stages 2 and 3. So, I'm > > >> wondering how the .xfm relates to the .lta and .m3z files...? > > >> > > >> Lastly, the particularly bad .xfm under v3.0.5 looks fine when created > > >> using v4.0.1. If we need or want accurate .xfm's would it be > > >> appropriate to run autorecon1 under v4 but then switch to v3 for > > >> autorecon2 & 3 so as to maintain compatibility with other subjects > > >> processed under v3? > > >> > > >> thanks, > > >> Mike H. > > >> > > >> > > >> > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how/where is talairach.xfm used?
Yes, based on a small N, version 4 does seem much more robust. So, if we wanted accurate .xfm's without requiring manual editing, would it be appropriate/fair to use v4 for autorecon1, but then use v3.0.5 for autorecon2 and 3, so as to maintain compatibility with other data processed under v3? thanks, Mike H. On Thu, 2007-10-11 at 17:30 -0400, Bruce Fischl wrote: > it's also worth noting that version 4 comes with Avi Snyder's most > excellent talairaching instead of the one we used to use, which in our > experience is *extremely* accurate and Robust (thanks Avi!). > > Bruce > > On Thu, 11 Oct > 2007, Doug Greve wrote: > > > It is not that important from a recon standpoint. However, if you intend to > > report talairach coods, create an average surface, or use that talairach > > transform in any way, it will be a problem. > > > > doug > > > > Michael Harms wrote: > > > >> Hello, > >> We are running FS v3.0.5 on some elderly brains, and the talairach > >> transform (as assessed via tkregister2 with fstal flag) is inaccurate in > >> an appreciable number of the scans we have examined so far. Frequently, > >> the inaccuracies involve primarily scaling or translation, although in > >> one instance the rotation was way-off (such that the cardinal axes were > >> basically swapped). However, even for this worst case, the white and > >> pial surfaces, as well as the aseg, look reasonable. (I haven't run > >> autorecon3 to create the surface parcellations yet). > >> > >> To what extent is talairach.xfm important for the autorecon2 & 3 stages? > >> If surfaces and aseg look ok, can an inaccurate talairach.xfm just be > >> ignored if we are not going to be averaging functional data? Will the > >> surface parcellations perhaps be affected somehow? > >> > >> Looking at ReconAllDevTable it appears that talairach.lta and > >> talairach.m3z are the primary inputs to stages 2 and 3. So, I'm > >> wondering how the .xfm relates to the .lta and .m3z files...? > >> > >> Lastly, the particularly bad .xfm under v3.0.5 looks fine when created > >> using v4.0.1. If we need or want accurate .xfm's would it be > >> appropriate to run autorecon1 under v4 but then switch to v3 for > >> autorecon2 & 3 so as to maintain compatibility with other subjects > >> processed under v3? > >> > >> thanks, > >> Mike H. > >> > >> > >> > > > > > ___ > 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] how/where is talairach.xfm used?
Is talairach.xfm even used as input for any stage of autorecon2 or 3? (Or, is it just the talairach.lta and talairach.m3z files?) thanks, Mike H. On Thu, 2007-10-11 at 16:28 -0400, Doug Greve wrote: > It is not that important from a recon standpoint. However, if you intend > to report talairach coods, create an average surface, or use that > talairach transform in any way, it will be a problem. > > doug > > Michael Harms wrote: > > >Hello, > >We are running FS v3.0.5 on some elderly brains, and the talairach > >transform (as assessed via tkregister2 with fstal flag) is inaccurate in > >an appreciable number of the scans we have examined so far. Frequently, > >the inaccuracies involve primarily scaling or translation, although in > >one instance the rotation was way-off (such that the cardinal axes were > >basically swapped). However, even for this worst case, the white and > >pial surfaces, as well as the aseg, look reasonable. (I haven't run > >autorecon3 to create the surface parcellations yet). > > > >To what extent is talairach.xfm important for the autorecon2 & 3 stages? > >If surfaces and aseg look ok, can an inaccurate talairach.xfm just be > >ignored if we are not going to be averaging functional data? Will the > >surface parcellations perhaps be affected somehow? > > > >Looking at ReconAllDevTable it appears that talairach.lta and > >talairach.m3z are the primary inputs to stages 2 and 3. So, I'm > >wondering how the .xfm relates to the .lta and .m3z files...? > > > >Lastly, the particularly bad .xfm under v3.0.5 looks fine when created > >using v4.0.1. If we need or want accurate .xfm's would it be > >appropriate to run autorecon1 under v4 but then switch to v3 for > >autorecon2 & 3 so as to maintain compatibility with other subjects > >processed under v3? > > > >thanks, > >Mike H. > > > > > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: [Analysis-bugs] 4.0.1 bug supposedly fixed with curvature
William, Freesurfer v3.0.5 is available for download from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/centos4_x86_64 Would it be possible for you to create a tarball of that subject and send it to me? I would like to try to recreate the problem here (as I am not able to recreate this problem using my own subject data). To create a tarball: cd $SUBJECTS_DIR tar zcvf subj.tgz subj (where 'subj' is the name of a subject) and then upload to me via the filedrop: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Nick On Fri, 2007-10-12 at 14:31 -0400, William R Mcgarry wrote: > Hello, >My name is William McGarry and I just submitted a bug report, but failed > to include the following: > > FREESURFER_HOME: /usr/local/freesurfer > Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 > RedHat release: Fedora Core release 5 (Bordeaux) > Kernel info: Linux 2.6.20-1.2320.fc5 x86_64 > > After updating to v4.0.0, the program would crash after trying to apply > curvature mapping with the following output: > reading white matter vertex locations... > % alloc: invalid block: 0xbb7760: 0 0 0 > > Abort > The curvature check box is also checked under "view," so we updated to v4.0.1 > which was supposed to fix this problem, yet it persists. This is an x86_64 > quad-core Xeon running Fedora Core 5 on the 64bit CentOS tksurfer > distribution. Please let us know if you have any information for work > arounds, updates, or if you could please provide us with a link to v3.0.5 > (the directory "Archive" is a bad link under > surfer.nmr.mgh.harvard.edu/pub/dist). Thank you. >Cordially, > William McGarry > ___ > Analysis-bugs mailing list > [EMAIL PROTECTED] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/analysis-bugs > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how/where is talairach.xfm used?
you could just rerun the tals with version 4 if you want. On Fri, 12 Oct 2007, Michael Harms wrote: Yes, based on a small N, version 4 does seem much more robust. So, if we wanted accurate .xfm's without requiring manual editing, would it be appropriate/fair to use v4 for autorecon1, but then use v3.0.5 for autorecon2 and 3, so as to maintain compatibility with other data processed under v3? thanks, Mike H. On Thu, 2007-10-11 at 17:30 -0400, Bruce Fischl wrote: it's also worth noting that version 4 comes with Avi Snyder's most excellent talairaching instead of the one we used to use, which in our experience is *extremely* accurate and Robust (thanks Avi!). Bruce On Thu, 11 Oct 2007, Doug Greve wrote: It is not that important from a recon standpoint. However, if you intend to report talairach coods, create an average surface, or use that talairach transform in any way, it will be a problem. doug Michael Harms wrote: Hello, We are running FS v3.0.5 on some elderly brains, and the talairach transform (as assessed via tkregister2 with fstal flag) is inaccurate in an appreciable number of the scans we have examined so far. Frequently, the inaccuracies involve primarily scaling or translation, although in one instance the rotation was way-off (such that the cardinal axes were basically swapped). However, even for this worst case, the white and pial surfaces, as well as the aseg, look reasonable. (I haven't run autorecon3 to create the surface parcellations yet). To what extent is talairach.xfm important for the autorecon2 & 3 stages? If surfaces and aseg look ok, can an inaccurate talairach.xfm just be ignored if we are not going to be averaging functional data? Will the surface parcellations perhaps be affected somehow? Looking at ReconAllDevTable it appears that talairach.lta and talairach.m3z are the primary inputs to stages 2 and 3. So, I'm wondering how the .xfm relates to the .lta and .m3z files...? Lastly, the particularly bad .xfm under v3.0.5 looks fine when created using v4.0.1. If we need or want accurate .xfm's would it be appropriate to run autorecon1 under v4 but then switch to v3 for autorecon2 & 3 so as to maintain compatibility with other subjects processed under v3? thanks, Mike H. ___ 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] selxavg3 memory error
Hi, I am trying to run an fMRI gamma analysis and am running into memory problems. I'm running freesurfer version stable 4.0 on unix through multnomah. The subject directory is located in /space/multnomah/3/users/gow/PROZ06/MRI/PROZ06004. We're running into issues with the selxavg-sess command. While in the /space/multnomah/3/users/gow/PROZ06/StudyDir I ran selxavg3-sess -sf sessid04 -df sesspar -analysis sm-gamma-fwhm5 -overwrite and got a memory error from matlab. Now this worked one time with using just one run, but when I try to analyze all three runs it returned the error and then when I went back and reran just that one run I received the same error. Below is my code. Thanks. multnomah:jsegawa[91] selxavg3-sess -sf sessid04 -df sesspar -analysis sm-gamma- fwhm5 -overwrite -- selxavg3-sess logfile is /autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/l og/selxavg3-sess-bold-sm-gamma-fwhm5-071012122828.log -- --- /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004 Fri Oct 12 12:28:28 EDT 2007 anadir = /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/sm-gamm a-fwhm5 analysis sm-gamma-fwhm5 alread exists for PROZ06004 ... reanalyzing (deleting old analysis) -- --- matlab output Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. Warning: MATLAB is starting without a display, using internal event queue. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2005 The MathWorks, Inc. Version 7.1.0.183 (R14) Service Pack 3 August 02, 2005 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Adding MNE Toolbox... >> >> >> >> >> >> >> /usr/local/freesurfer/stable4/fsfast/toolbox/fast_selxavg3. m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2 .1 2007/09/27 15:25:58 greve Exp $ outtop = /autofs/space/multnomah_003/users/gow/PROZ06/MRI Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 simple-v-complex.mat Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. nruns = 1 autostimdur = 1 outanadir = /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/sm-g amma-fwhm5 Found 49490/110592 (44.8) voxels in mask Creating Design Matrix Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. ntptot = 414, nX = 8, DOF = 406 XCond = 288.38 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.501599(t=0.113866) 2 -0.25 -0.257524(t=0.220947) 3 0 -0.0157544(t=0.325266) 4 0.25 0.221692(t=0.429817) 5 0.5 0.449162(t=0.537974) AR1 Correction M: 0.0218428 1.0499 Computing contrast matrices Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. 1 simple-v-complex J= 1 eff = 78.7 vrf = 78.7205 vrfffx = 78.7205 r = 1. 00 OLS Beta Pass run 1t= 0.0 Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. Global In-Mask Mean = 544.358 Rescale Target = 100 RescaleFactor = 0.183703 OLS Residual Pass run 1t= 0.0 Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. ??? Error using ==> unknown Out of memory. Type HELP MEMORY for your options. Error in ==> fast_selxavg3 at 417 rho1run = sum(rrun(1:end-1,:).*rrun(2:end,:))./rsserun; >> -- ERROR: fast_selxavg3() failed\n multnomah:jsegawa[92] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] model for pair-T test
The --paired-diff options just take the difference between adjacently specfied inputs. You then set up your design matrix or FSGD file and then run mri_glmfit. The --help for mri_glmfit has a lot of info about the glm analysis. If you just want to test whether the difference is 0, you can use the --osgm flag (one-sample group mean). doug Wang, Xin wrote: Please give me more detailed explanations of how to run mris_preproc --paired-diff or (--paired-diff-norm)? and how to setup the GLM after run this commend? I could not find needed information on the website. Thank you very much. Xin From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 10/5/2007 5:20 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] model for pair-T test Can you use the --paired-diff to mris_preproc? Wang, Xin wrote: Hello, group, Could anybody tell me how to do the pair T test and the repeat measurement F test? I will really appreciate if you can share the steps and GLM of the tests. I am using the old freesurfer group analysis. Thank you, very much, Xin Wang ___ 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 [EMAIL PROTECTED] 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] selxavg3 memory error
You're probably going to need a computer with more memory. That one only has 1G. doug [EMAIL PROTECTED] wrote: Hi, I am trying to run an fMRI gamma analysis and am running into memory problems. I'm running freesurfer version stable 4.0 on unix through multnomah. The subject directory is located in /space/multnomah/3/users/gow/PROZ06/MRI/PROZ06004. We're running into issues with the selxavg-sess command. While in the /space/multnomah/3/users/gow/PROZ06/StudyDir I ran selxavg3-sess -sf sessid04 -df sesspar -analysis sm-gamma-fwhm5 -overwrite and got a memory error from matlab. Now this worked one time with using just one run, but when I try to analyze all three runs it returned the error and then when I went back and reran just that one run I received the same error. Below is my code. Thanks. multnomah:jsegawa[91] selxavg3-sess -sf sessid04 -df sesspar -analysis sm-gamma- fwhm5 -overwrite -- selxavg3-sess logfile is /autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/l og/selxavg3-sess-bold-sm-gamma-fwhm5-071012122828.log -- --- /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004 Fri Oct 12 12:28:28 EDT 2007 anadir = /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/sm-gamm a-fwhm5 analysis sm-gamma-fwhm5 alread exists for PROZ06004 ... reanalyzing (deleting old analysis) -- --- matlab output Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. Warning: MATLAB is starting without a display, using internal event queue. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2005 The MathWorks, Inc. Version 7.1.0.183 (R14) Service Pack 3 August 02, 2005 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Adding MNE Toolbox... /usr/local/freesurfer/stable4/fsfast/toolbox/fast_selxavg3. m $Id: fast_selxavg3.m,v 1.55.2 .1 2007/09/27 15:25:58 greve Exp $ outtop = /autofs/space/multnomah_003/users/gow/PROZ06/MRI Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 simple-v-complex.mat Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. nruns = 1 autostimdur = 1 outanadir = /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/sm-g amma-fwhm5 Found 49490/110592 (44.8) voxels in mask Creating Design Matrix Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. ntptot = 414, nX = 8, DOF = 406 XCond = 288.38 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.501599(t=0.113866) 2 -0.25 -0.257524(t=0.220947) 3 0 -0.0157544(t=0.325266) 4 0.25 0.221692(t=0.429817) 5 0.5 0.449162(t=0.537974) AR1 Correction M: 0.0218428 1.0499 Computing contrast matrices Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. 1 simple-v-complex J= 1 eff = 78.7 vrf = 78.7205 vrfffx = 78.7205 r = 1. 00 OLS Beta Pass run 1t= 0.0 Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. Global In-Mask Mean = 544.358 Rescale Target = 100 RescaleFactor = 0.183703 OLS Residual Pass run 1t= 0.0 Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. ??? Error using ==> unknown Out of memory. Type HELP MEMORY for your options. Error in ==> fast_selxavg3 at 417 rho1run = sum(rrun(1:end-1,:).*rrun(2:end,:))./rsserun; -- ERROR: fast_selxavg3() failed\n multnomah:jsegawa[92] ___ 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 [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mincinfo broken pipe
Hi Chuck, is that partition full? Bruce On Fri, 12 Oct 2007, Chuck Theobald wrote: Hi, Following some system upgrade to our Linux 2.6 systems, freesurfer has ceased to work. When running recon-all on bert, we get a message referring to a broken pipe and a crash in mincinfo. We are running Gentoo: doolin ~ # uname -a Linux doolin 2.6.21-gentoo-r4 #1 SMP Thu Aug 9 09:33:11 PDT 2007 i686 AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ AuthenticAMD GNU/Linux doolin ~ # Any help and/or advice would be appreciated. Thank you, Chuck mri_add_xform_to_header -c /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/transforms/talairach.xfm /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/orig.mgz /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/orig.mgz INFO: extension is mgz # [EMAIL PROTECTED] Nu Intensity Correction Fri Oct 12 10:37:03 PDT 2007 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.3.2.1 2006/11/24 20:16:38 nicks Exp $ Linux doolin 2.6.21-gentoo-r4 #1 SMP Thu Aug 9 09:33:11 PDT 2007 i686 AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ AuthenticAMD GNU/Linux Fri Oct 12 10:37:03 PDT 2007 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED] (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.28553 /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28553/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28553/nu0.mnc reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.28553/nu0.mnc... Iteration 1 Fri Oct 12 10:37:11 PDT 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.28553/nu0.mnc ./tmp.mri_nu_correct.mni.28553/nu1.mnc [EMAIL PROTECTED]:/vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/] [2007-10-12 10:37:11] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_28603/ ./tmp.mri_nu_correct.mni.28553/nu0.mnc ./tmp.mri_nu_correct.mni.28553/nu1.imp nu_estimate_np_and_em: broken pipe nu_estimate_np_and_em: crashed while running mincinfo (termination status=13) nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Linux doolin 2.6.21-gentoo-r4 #1 SMP Thu Aug 9 09:33:11 PDT 2007 i686 AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ AuthenticAMD GNU/Linux recon-all exited with ERRORS at Fri Oct 12 10:37:11 PDT 2007 [EMAIL PROTECTED] /usr/local/freesurfer $ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mincinfo broken pipe
Hi, Following some system upgrade to our Linux 2.6 systems, freesurfer has ceased to work. When running recon-all on bert, we get a message referring to a broken pipe and a crash in mincinfo. We are running Gentoo: doolin ~ # uname -a Linux doolin 2.6.21-gentoo-r4 #1 SMP Thu Aug 9 09:33:11 PDT 2007 i686 AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ AuthenticAMD GNU/Linux doolin ~ # Any help and/or advice would be appreciated. Thank you, Chuck mri_add_xform_to_header -c /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/transforms/talairach.xfm /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/orig.mgz /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/orig.mgz INFO: extension is mgz # [EMAIL PROTECTED] Nu Intensity Correction Fri Oct 12 10:37:03 PDT 2007 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.3.2.1 2006/11/24 20:16:38 nicks Exp $ Linux doolin 2.6.21-gentoo-r4 #1 SMP Thu Aug 9 09:33:11 PDT 2007 i686 AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ AuthenticAMD GNU/Linux Fri Oct 12 10:37:03 PDT 2007 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED] (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.28553 /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28553/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28553/nu0.mnc reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.28553/nu0.mnc... Iteration 1 Fri Oct 12 10:37:11 PDT 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.28553/nu0.mnc ./tmp.mri_nu_correct.mni.28553/nu1.mnc [EMAIL PROTECTED]:/vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/] [2007-10-12 10:37:11] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_28603/ ./tmp.mri_nu_correct.mni.28553/nu0.mnc ./tmp.mri_nu_correct.mni.28553/nu1.imp nu_estimate_np_and_em: broken pipe nu_estimate_np_and_em: crashed while running mincinfo (termination status=13) nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Linux doolin 2.6.21-gentoo-r4 #1 SMP Thu Aug 9 09:33:11 PDT 2007 i686 AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ AuthenticAMD GNU/Linux recon-all exited with ERRORS at Fri Oct 12 10:37:11 PDT 2007 [EMAIL PROTECTED] /usr/local/freesurfer $ -- Chuck Theobald System Administrator The Robert and Beverly Lewis Center for Neuroimaging University of Oregon P: 541-346-0343 F: 541-346-0345 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mincinfo broken pipe
you might check the MNI list to see if this is a known issue for them. On Fri, 12 Oct 2007, Chuck Theobald wrote: Hi, No, we have sufficient disk space on each machine. This used to work, but started failing following upgrades to system files. I suspect libc.so.6 or libm.so.6, since mincinfo is linked to both, and both were part of the upgrade, but I don't have anything specific pointing to this as the cause. Chuck Bruce Fischl wrote: Hi Chuck, is that partition full? Bruce ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mincinfo broken pipe
Chuck, Which freesurfer is installed? The rh9 freesurfer dist is built against libstdc++.so.5 (which many systems dont have), whereas the centos freesurfer dist uses .6. Nick On Fri, 2007-10-12 at 14:13 -0700, Chuck Theobald wrote: > Hi, > > No, we have sufficient disk space on each machine. > > This used to work, but started failing following upgrades to system > files. I suspect libc.so.6 or libm.so.6, since mincinfo is linked to > both, and both were part of the upgrade, but I don't have anything > specific pointing to this as the cause. > > Chuck > > > Bruce Fischl wrote: > > Hi Chuck, > > > > is that partition full? > > > > Bruce > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mincinfo broken pipe
Hi, No, we have sufficient disk space on each machine. This used to work, but started failing following upgrades to system files. I suspect libc.so.6 or libm.so.6, since mincinfo is linked to both, and both were part of the upgrade, but I don't have anything specific pointing to this as the cause. Chuck Bruce Fischl wrote: Hi Chuck, is that partition full? Bruce -- Chuck Theobald System Administrator The Robert and Beverly Lewis Center for Neuroimaging University of Oregon P: 541-346-0343 F: 541-346-0345 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mincinfo broken pipe
I believe we are using the CentOS version. I am downloading the RH9 distro for version 3.0.3 to see if that will work for us. Chuck Nick Schmansky wrote: Chuck, Which freesurfer is installed? The rh9 freesurfer dist is built against libstdc++.so.5 (which many systems dont have), whereas the centos freesurfer dist uses .6. Nick -- Chuck Theobald System Administrator The Robert and Beverly Lewis Center for Neuroimaging University of Oregon P: 541-346-0343 F: 541-346-0345 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
