[Freesurfer] R: Re: TRACULA
Hi and thank you very much for your availability. Now, I'm running tracula as following: trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01 my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used in previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the same that I have previously used in FSL analysis. Please, my questions are:a- Are correct the command and the files (dyrectory positioning and their extensions)?b- Now my computer seem to running but after 1 h from the start, I visualize on my desktop this message Your Mac 0SX has no more space available for application memory.My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 MHz DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of 999,35 I have download the package for (Snow)Leopard (10.5/6.x) Intel. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 27-gen-2013 19.36 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] TRACULA Hi Stefano - The -prep option doesn't take an argument. Please run trac-all with no arguments to see usage info. a.y Hi list, I'm trying to run a test subject with TRACULA. I placed a folder in /Applications/freesurfer/subject/subject_prova which contains these files: data.nii.gz (DWI), bvals and bvecs (as used in previous FSL analysis) and T1-images.in /Applications/freesurfer/subject/subject_prova This is the command that I'm running:[iMac-di-Stefano:~] Stefano% trac-all -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i $FREESURFER_HOME/subjects/subject_prova ERROR: flag /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep /Applications/freesurfer/subjects/subject_prova/CON_01 --i /Applications/freesurfer/subjects/subject_prova Please, give me an help. Thanks in advance, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] R: R: Re: TRACULA
Hi and thank you very much for your availability. Now, I'm running tracula as following: trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01 my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used in previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the same that I have previously used in FSL analysis. Please, my questions are:a- Are correct the command and the files (dyrectory positioning and their extensions)?b- Now my computer seem to running but after 1 h from the start, I visualize on my desktop this message Your Mac 0SX has no more space available for application memory.My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 MHz DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of 999,35 I have download the package for (Snow)Leopard (10.5/6.x) Intel. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 27-gen-2013 19.36 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] TRACULA Hi Stefano - The -prep option doesn't take an argument. Please run trac-all with no arguments to see usage info. a.y Hi list, I'm trying to run a test subject with TRACULA. I placed a folder in /Applications/freesurfer/subject/subject_prova which contains these files: data.nii.gz (DWI), bvals and bvecs (as used in previous FSL analysis) and T1-images.in /Applications/freesurfer/subject/subject_prova This is the command that I'm running:[iMac-di-Stefano:~] Stefano% trac-all -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i $FREESURFER_HOME/subjects/subject_prova ERROR: flag /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep /Applications/freesurfer/subjects/subject_prova/CON_01 --i /Applications/freesurfer/subjects/subject_prova Please, give me an help. Thanks in advance, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] R: R: Re: TRACULA
Hi Stefano - The argument of the -c option is a configuration file, not a directory. For more info on trac-all and setting up the configuration file, please see the trac-all wiki page: http://www.freesurfer.net/fswiki/trac-all and tracula tutorials: http://www.freesurfer.net/fswiki/FsTutorial/Tracula a.y On Mon, 28 Jan 2013, std...@virgilio.it wrote: Hi and thank you very much for your availability. Now, I'm running tracula as following: trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01 my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used in previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the same that I have previously used in FSL analysis. Please, my questions are: a- Are correct the command and the files (dyrectory positioning and their extensions)? b- Now my computer seem to running but after 1 h from the start, I visualize on my desktop this message Your Mac 0SX has no more space available for application memory. My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 MHz DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of 999,35 I have download the package for (Snow)Leopard (10.5/6.x) Intel. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 27-gen-2013 19.36 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] TRACULA Hi Stefano - The -prep option doesn't take an argument. Please run trac-all with no arguments to see usage info. a.y Hi list, I'm trying to run a test subject with TRACULA. I placed a folder in /Applications/freesurfer/subject/subject_prova which contains these files: data.nii.gz (DWI), bvals and bvecs (as used in previous FSL analysis) and T1-images.in /Applications/freesurfer/subject/subject_prova This is the command that I'm running:[iMac-di-Stefano:~] Stefano% trac-all -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i $FREESURFER_HOME/subjects/subject_prova ERROR: flag /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep /Applications/freesurfer/subjects/subject_prova/CON_01 --i /Applications/freesurfer/subjects/subject_prova Please, give me an help. Thanks in advance, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] xhemi problem
The second command is probably failing because the first command is failing. The 1st is failing because you don't have GLIBC 2.4. I'll have to leave that one for Nick or Zeke. doug On 01/26/2013 03:21 PM, Gabriel Gonzalez Escamilla wrote: Well there is actually two kinds of error: 1) when I run surfreg --s c_003 --t fsaverage_sym --lh and then: surfreg --s c_003 --t fsaverage_sym --lh --xhemi sáb ene 26 21:09:21 CET 2013 setenv SUBJECTS_DIR /root/trabajo/freesurfer/subjects cd /root /root/trabajo/freesurfer/bin/surfreg --s c_003 --t fsaverage_sym --lh --xhemi Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux xhemi does not exist for c_003, running now xhemireg --s c_003 outdir is /root/trabajo/freesurfer/subjects/c_003/xhemi Logfile is /root/trabajo/freesurfer/subjects/c_003/xhemi/xhemireg.lh.log /root/trabajo/freesurfer/bin/xhemireg --s c_003 $Id: xhemireg,v 1.23 2012/06/04 15:00:51 greve Exp $ sáb ene 26 21:09:21 CET 2013 Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux /root/trabajo/freesurfer/subjects/c_003 setenv SUBJECTS_DIR /root/trabajo/freesurfer/subjects sáb ene 26 21:09:21 CET 2013 sáb ene 26 21:09:21 CET 2013 mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/orig.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/orig.mgz targvol mri/orig.mgz outvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/orig.mgz regfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat invert 0 tal0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1360182876 Final tkRAS-to-tkRAS Matrix is: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: -1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/T1.mgz --targ mri/T1.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/T1.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/T1.mgz targvol mri/T1.mgz outvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/T1.mgz regfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat invert 0 tal0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1359747149 Final tkRAS-to-tkRAS Matrix is: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: -1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/brain.mgz --targ mri/brain.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/brain.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/brain.mgz targvol mri/brain.mgz outvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/brain.mgz regfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat invert 0 tal0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1359336383 Final tkRAS-to-tkRAS Matrix is: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: -1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/brainmask.mgz --targ mri/brainmask.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/brainmask.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000
Re: [Freesurfer] xhemi problem
Thanks Doug for your answerBut, always the first one ends properlysurfreg --s c_003 --t fsaverage_sym --lhit's the second one that have two different errors:surfreg --s c_003 --t fsaverage_sym --lh --xhemiAnd yes you are right, it says that it's because of the library but, the original mri_convert did't have that trouble. I have also tried to excecute the command xhemireg but didn't work either.Thanks,GabrielEl 28/01/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:The second command is probably failing because the first command is failing. The 1st is failing because you don't have GLIBC 2.4. I'll have to leave that one for Nick or Zeke.dougOn 01/26/2013 03:21 PM, Gabriel Gonzalez Escamilla wrote:Well there is actually two kinds of error:1) when I runsurfreg --s c_003 --t fsaverage_sym --lhand then:surfreg --s c_003 --t fsaverage_sym --lh --xhemisáb ene 26 21:09:21 CET 2013setenv SUBJECTS_DIR /root/trabajo/freesurfer/subjectscd /root/root/trabajo/freesurfer/bin/surfreg --s c_003 --t fsaverage_sym --lh --xhemiLinux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxxhemi does not exist for c_003, running nowxhemireg --s c_003outdir is /root/trabajo/freesurfer/subjects/c_003/xhemiLogfile is /root/trabajo/freesurfer/subjects/c_003/xhemi/xhemireg.lh.log/root/trabajo/freesurfer/bin/xhemireg--s c_003$Id: xhemireg,v 1.23 2012/06/04 15:00:51 greve Exp $sáb ene 26 21:09:21 CET 2013Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux/root/trabajo/freesurfer/subjects/c_003setenv SUBJECTS_DIR /root/trabajo/freesurfer/subjectssáb ene 26 21:09:21 CET 2013sáb ene 26 21:09:21 CET 2013mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/orig.mgz --keep-precision --no-save-regMatrix from regfile:-1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;movvol mri/orig.mgztargvol mri/orig.mgzoutvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/orig.mgzregfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.datinvert 0tal 0talres 2regheader 0noresample 0interp trilinear (1)precision uchar (0)Gdiag_no -1Synth 0SynthSeed 1360182876Final tkRAS-to-tkRAS Matrix is:-1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;Vox2Vox Matrix is:-1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;ResamplingOutput registration matrix is identitymri_vol2vol donemri_vol2vol --mov mri/T1.mgz --targ mri/T1.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/T1.mgz --keep-precision --no-save-regMatrix from regfile:-1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;movvol mri/T1.mgztargvol mri/T1.mgzoutvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/T1.mgzregfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.datinvert 0tal 0talres 2regheader 0noresample 0interp trilinear (1)precision uchar (0)Gdiag_no -1Synth 0SynthSeed 1359747149Final tkRAS-to-tkRAS Matrix is:-1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;Vox2Vox Matrix is:-1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;ResamplingOutput registration matrix is identitymri_vol2vol donemri_vol2vol --mov mri/brain.mgz --targ mri/brain.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/brain.mgz --keep-precision --no-save-regMatrix from regfile:-1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;movvol mri/brain.mgztargvol mri/brain.mgzoutvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/brain.mgzregfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.datinvert 0tal 0talres 2regheader 0noresample 0interp trilinear (1)precision uchar (0)Gdiag_no -1Synth 0SynthSeed 1359336383Final tkRAS-to-tkRAS Matrix is:-1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;Vox2Vox Matrix is:-1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;ResamplingOutput registration matrix is identitymri_vol2vol donemri_vol2vol --mov mri/brainmask.mgz --targ mri/brainmask.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o
Re: [Freesurfer] nu_estimate_np_and_em error during recon-all
Dear Nick, I was wondering whether you (or indeed anyone else reading this!) know where the error that I report earlier in this thread might be coming from. Many thanks in advance! Tudor On 20 December 2012 05:27, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Tudor, I don't know how to solve this problem. Maybe Nick knows. doug On 12/19/12 6:59 AM, Tudor Popescu wrote: Hi Doug, thanks for replying, here is the file attached. In case the attachment doesn't go through please let me know if I should send it to a different address. Tudor On 18 December 2012 17:34, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Can you send the recon-all.log file (located in the subject/scripts folder). doug On 12/18/2012 11:41 AM, Tudor Popescu wrote: Hello, First of all, apologies for asking for help three times today! THings will hopefully become clearer once I get used to FS a bit; I really do appreciate the amazing support provided by the team behind FreeSurfer! I ran the following command on one of my structurals: /recon-all -subject M01 -i M01.nii.gz -all/ After a few minutes, recon-all ended with the following message: /Assertion failed at line 827 in file templates/CachedArray.cc/ /nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)/ /nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)/ /ERROR: nu_correct/ /Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux/ I apologise for reporting an error that's already been reported in the past, but unfortunately the solutions suggested in those past threads did not work in my case. To address a few of them: * my PATH (listed below) does not seem to include two MNI installations //home/virtualuser/freesurfer/bin:/home/virtualuser/freesurfer/fsfast/bin:/home/virtualuser/freesurfer/tktools:/home/virtualuser/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games/ * the version of FreeSurfer that I installed is the latest disk image available on the website (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full) - I did not see any dev version that would presumably include any missing libraries presumably implied by the above error * I tried updating the Xubuntu inside my VirtualBox, however it reports an insufficient space problem that from I can see does not have a trivial fix Advance thanks for any help! Tudor ___ 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. recon-all.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] nu_estimate_np_and_em error during recon-all
Tudor, Greg, and Petr, I'm currently attempting to replicate this problem. In the meantime, can you tell me which Windows and which VirtualBox version you are running this on? I'm at a loss as to why this build no longer works. Nick On Mon, 2013-01-28 at 18:19 +, Tudor Popescu wrote: Dear Nick, I was wondering whether you (or indeed anyone else reading this!) know where the error that I report earlier in this thread might be coming from. Many thanks in advance! Tudor On 20 December 2012 05:27, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Tudor, I don't know how to solve this problem. Maybe Nick knows. doug On 12/19/12 6:59 AM, Tudor Popescu wrote: Hi Doug, thanks for replying, here is the file attached. In case the attachment doesn't go through please let me know if I should send it to a different address. Tudor On 18 December 2012 17:34, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you send the recon-all.log file (located in the subject/scripts folder). doug On 12/18/2012 11:41 AM, Tudor Popescu wrote: Hello, First of all, apologies for asking for help three times today! THings will hopefully become clearer once I get used to FS a bit; I really do appreciate the amazing support provided by the team behind FreeSurfer! I ran the following command on one of my structurals: /recon-all -subject M01 -i M01.nii.gz -all/ After a few minutes, recon-all ended with the following message: /Assertion failed at line 827 in file templates/CachedArray.cc/ /nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)/ /nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)/ /ERROR: nu_correct/ /Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux/ I apologise for reporting an error that's already been reported in the past, but unfortunately the solutions suggested in those past threads did not work in my case. To address a few of them: * my PATH (listed below) does not seem to include two MNI installations //home/virtualuser/freesurfer/bin:/home/virtualuser/freesurfer/fsfast/bin:/home/virtualuser/freesurfer/tktools:/home/virtualuser/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games/ * the version of FreeSurfer that I installed is the latest disk image available on the website (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full) - I did not see any dev version that would presumably include any missing libraries presumably implied by the above error * I tried updating the Xubuntu inside my VirtualBox, however it reports an insufficient space problem that from I can see does not have a trivial fix Advance thanks for any help! Tudor ___ 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
[Freesurfer] R: Re: R: R: Re: TRACULA
Thank you very much for you kindness Anastasia. The folder that contains .nii.gz file is correct?I'm looking the recommended trac-all update. Where can I put it? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 28-gen-2013 16.45 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: TRACULA Hi Stefano - The argument of the -c option is a configuration file, not a directory. For more info on trac-all and setting up the configuration file, please see the trac-all wiki page: http://www.freesurfer.net/fswiki/trac-all and tracula tutorials: http://www.freesurfer.net/fswiki/FsTutorial/Tracula a.y On Mon, 28 Jan 2013, std...@virgilio.it wrote: Hi and thank you very much for your availability. Now, I'm running tracula as following: trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01 my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used in previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the same that I have previously used in FSL analysis. Please, my questions are: a- Are correct the command and the files (dyrectory positioning and their extensions)? b- Now my computer seem to running but after 1 h from the start, I visualize on my desktop this message Your Mac 0SX has no more space available for application memory. My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 MHz DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of 999,35 I have download the package for (Snow)Leopard (10.5/6.x) Intel. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 27-gen-2013 19.36 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] TRACULA Hi Stefano - The -prep option doesn't take an argument. Please run trac-all with no arguments to see usage info. a.y Hi list, I'm trying to run a test subject with TRACULA. I placed a folder in /Applications/freesurfer/subject/subject_prova which contains these files: data.nii.gz (DWI), bvals and bvecs (as used in previous FSL analysis) and T1-images.in /Applications/freesurfer/subject/subject_prova This is the command that I'm running:[iMac-di-Stefano:~] Stefano% trac-all -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i $FREESURFER_HOME/subjects/subject_prova ERROR: flag /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep /Applications/freesurfer/subjects/subject_prova/CON_01 --i /Applications/freesurfer/subjects/subject_prova Please, give me an help. Thanks in advance, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] nu_estimate_np_and_em error during recon-all
Hi Nick, Thanks for your help, I'm on Windows XP SP3 VirtualBox 4.2.4 Tudor On 28 January 2013 18:30, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Tudor, Greg, and Petr, I'm currently attempting to replicate this problem. In the meantime, can you tell me which Windows and which VirtualBox version you are running this on? I'm at a loss as to why this build no longer works. Nick On Mon, 2013-01-28 at 18:19 +, Tudor Popescu wrote: Dear Nick, I was wondering whether you (or indeed anyone else reading this!) know where the error that I report earlier in this thread might be coming from. Many thanks in advance! Tudor On 20 December 2012 05:27, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Tudor, I don't know how to solve this problem. Maybe Nick knows. doug On 12/19/12 6:59 AM, Tudor Popescu wrote: Hi Doug, thanks for replying, here is the file attached. In case the attachment doesn't go through please let me know if I should send it to a different address. Tudor On 18 December 2012 17:34, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you send the recon-all.log file (located in the subject/scripts folder). doug On 12/18/2012 11:41 AM, Tudor Popescu wrote: Hello, First of all, apologies for asking for help three times today! THings will hopefully become clearer once I get used to FS a bit; I really do appreciate the amazing support provided by the team behind FreeSurfer! I ran the following command on one of my structurals: /recon-all -subject M01 -i M01.nii.gz -all/ After a few minutes, recon-all ended with the following message: /Assertion failed at line 827 in file templates/CachedArray.cc/ /nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)/ /nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)/ /ERROR: nu_correct/ /Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux/ I apologise for reporting an error that's already been reported in the past, but unfortunately the solutions suggested in those past threads did not work in my case. To address a few of them: * my PATH (listed below) does not seem to include two MNI installations //home/virtualuser/freesurfer/bin:/home/virtualuser/freesurfer/fsfast/bin:/home/virtualuser/freesurfer/tktools:/home/virtualuser/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games/ * the version of FreeSurfer that I installed is the latest disk image available on the website (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full) - I did not see any dev version that would presumably include any missing libraries presumably implied by the above error * I tried updating the Xubuntu inside my VirtualBox, however it reports an insufficient space problem that from I can see does not have a trivial fix Advance thanks for any help! Tudor ___ 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:
Re: [Freesurfer] R: Re: R: R: Re: TRACULA
Hi Stefano - Type which trac-all to find out where trac-all lives on your computer, then copy the updated version over it. a.y On Mon, 28 Jan 2013, std...@virgilio.it wrote: Thank you very much for you kindness Anastasia. The folder that contains .nii.gz file is correct? I'm looking the recommended trac-all update. Where can I put it? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 28-gen-2013 16.45 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: TRACULA Hi Stefano - The argument of the -c option is a configuration file, not a directory. For more info on trac-all and setting up the configuration file, please see the trac-all wiki page: http://www.freesurfer.net/fswiki/trac-all and tracula tutorials: http://www.freesurfer.net/fswiki/FsTutorial/Tracula a.y On Mon, 28 Jan 2013, std...@virgilio.it wrote: Hi and thank you very much for your availability. Now, I'm running tracula as following: trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01 my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used in previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the same that I have previously used in FSL analysis. Please, my questions are: a- Are correct the command and the files (dyrectory positioning and their extensions)? b- Now my computer seem to running but after 1 h from the start, I visualize on my desktop this message Your Mac 0SX has no more space available for application memory. My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 MHz DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of 999,35 I have download the package for (Snow)Leopard (10.5/6.x) Intel. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 27-gen-2013 19.36 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] TRACULA Hi Stefano - The -prep option doesn't take an argument. Please run trac-all with no arguments to see usage info. a.y Hi list, I'm trying to run a test subject with TRACULA. I placed a folder in /Applications/freesurfer/subject/subject_prova which contains these files: data.nii.gz (DWI), bvals and bvecs (as used in previous FSL analysis) and T1-images.in /Applications/freesurfer/subject/subject_prova This is the command that I'm running:[iMac-di-Stefano:~] Stefano% trac-all -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i $FREESURFER_HOME/subjects/subject_prova ERROR: flag /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep /Applications/freesurfer/subjects/subject_prova/CON_01 --i /Applications/freesurfer/subjects/subject_prova Please, give me an help. Thanks in advance, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Skull Striping
Dear all, I am currently working on a 1.5T SPGR 1.5mm MRI longitudinal dataset, and I would like to know if one is expected to manually skull strip the images before de recon -all procedure. I am aware that the image quality may be a limiting factor for the freesurfer processing. Regards, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mgh conversion
How many vertices are on the surface? For nifti you have to reshape the size of the image so that it fits in the nifti format (requires each dim be less than 32k). If the number of vertices has a prime factor that is more than 32k, then you cannot convert it to nifti and use it in another software package (it still works in FreeSurfer, but then you could just use an mgh file then). doug On 01/28/2013 01:58 PM, Courtney Haswell wrote: Hi, Was there a resolution to this thread on the FreeSurfer mail archive? http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17886.html I am having the same issue trying to convert a cortical thickness sig.mgh to a NIfTI file. I want to use the statistically significant area as an ROI in another analysis. Thanks, Courtney Haswell -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Skull Striping
Hi Pedro, you should run it through recon-all and see how the automatic skull stripping does, then correct it if necessary. doug On 01/28/2013 02:08 PM, Pedro Rosa wrote: Dear all, I am currently working on a 1.5T SPGR 1.5mm MRI longitudinal dataset, and I would like to know if one is expected to manually skull strip the images before de recon -all procedure. I am aware that the image quality may be a limiting factor for the freesurfer processing. Regards, Pedro Rosa. ___ 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all v5.2 slightly changed
hello all, Just for reference, we were having an issue with recon-all v 5.2 exiting with errors due to issues with the perirhinal cortex. We were able to simply commented out the parts of the script dealing with the perirhinal cortex. Just an FYI to those who may be having a similar problem. Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all v5.2 slightly changed
Hi Jon what were the errors? We will want to fix them prior to official release. thanks Bruce On Mon, 28 Jan 2013, Jonathan Holt wrote: hello all, Just for reference, we were having an issue with recon-all v 5.2 exiting with errors due to issues with the perirhinal cortex. We were able to simply commented out the parts of the script dealing with the perirhinal cortex. Just an FYI to those who may be having a similar problem. Jon ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all v5.2 slightly changed
Jon, If the error is where the perirhinal labels cannot be found in the fsaverage that sits in your subjects dir, then that issue was fixed on a more recent beta 5.2. recon-all now checks if the perirhinal labels exist in the fsaverage found in the subjects dir (which might not be the case if running on prior data where the copy of fsaverage was made) and if the labels do not exist it creates a new link. What that this issue? or a new one? Nick On Mon, 2013-01-28 at 14:50 -0500, Bruce Fischl wrote: Hi Jon what were the errors? We will want to fix them prior to official release. thanks Bruce On Mon, 28 Jan 2013, Jonathan Holt wrote: hello all, Just for reference, we were having an issue with recon-all v 5.2 exiting with errors due to issues with the perirhinal cortex. We were able to simply commented out the parts of the script dealing with the perirhinal cortex. Just an FYI to those who may be having a similar problem. Jon ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all v5.2 slightly changed
Also, could I have a link for the centos4 of this updated version of 5.2? And is there a working 5.2 for Mac OS X, 10.7 or 10.8 specifically? jon On Jan 28, 2013, at 3:19 PM, Jonathan Holt wrote: Nick, it was in fact an error with missing perirhinal cortex labels in fsaverage. It did not exist, and then the process exited. Good to know it's been fixed. jon On Jan 28, 2013, at 2:48 PM, Jonathan Holt wrote: hello all, Just for reference, we were having an issue with recon-all v 5.2 exiting with errors due to issues with the perirhinal cortex. We were able to simply commented out the parts of the script dealing with the perirhinal cortex. Just an FYI to those who may be having a similar problem. Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all v5.2 slightly changed
Nick, it was in fact an error with missing perirhinal cortex labels in fsaverage. It did not exist, and then the process exited. Good to know it's been fixed. jon On Jan 28, 2013, at 2:48 PM, Jonathan Holt wrote: hello all, Just for reference, we were having an issue with recon-all v 5.2 exiting with errors due to issues with the perirhinal cortex. We were able to simply commented out the parts of the script dealing with the perirhinal cortex. Just an FYI to those who may be having a similar problem. Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all v5.2 slightly changed
updated 5.2 versions for centos4_x86_64 and macos lion are here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/ an updated centos4 build (32b) will not be ready until tomorrow. n. On Mon, 2013-01-28 at 15:29 -0500, Jonathan Holt wrote: Also, could I have a link for the centos4 of this updated version of 5.2? And is there a working 5.2 for Mac OS X, 10.7 or 10.8 specifically? jon On Jan 28, 2013, at 3:19 PM, Jonathan Holt wrote: Nick, it was in fact an error with missing perirhinal cortex labels in fsaverage. It did not exist, and then the process exited. Good to know it's been fixed. jon On Jan 28, 2013, at 2:48 PM, Jonathan Holt wrote: hello all, Just for reference, we were having an issue with recon-all v 5.2 exiting with errors due to issues with the perirhinal cortex. We were able to simply commented out the parts of the script dealing with the perirhinal cortex. Just an FYI to those who may be having a similar problem. Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] R: Re: R: Re: R: R: Re: TRACULA
Hi Anastasia, I have prepared this configuration file: ## Set locations of diffusion DICOMs, diffusion output, FreeSurfer recons## This file contains commands that will be run by trac-all before an analysis.# It is used to set all parameters needed for the analysis.## Remove a parameter from your dmrirc file if you want to use the default value.# Parameters that don't have default values must be specified.## Any other commands that you might want to run before an analysis can be added# to this file.## Original Author: Anastasia Yendiki# CVS Revision Info:#$Author: ayendiki $# $Date: 2010/12/15 08:36:00 $#$Revision: 1.1 $## Copyright (C) 2010# The General Hospital Corporation (Boston, MA).# All rights reserved.## Distribution, usage and copying of this software is covered under the# terms found in the License Agreement file named 'COPYING' found in the# FreeSurfer source code root directory, and duplicated here:# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense## General inquiries: freesurfer@nmr.mgh.harvard.edu## FreeSurfer SUBJECTS_DIR# setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/subject_prova# Output directory where trac-all results will be savedset dtroot = $SUBJECTS_DIR# Subject IDsset subjlist = (Diff01)set runlist = (1)# Input diffusion DICOMs (file names relative to dcmroot)set dcmroot = $SUBJECTS_DIRset dcmlist = (Diff01/data.nii.gz)set bvalfile = $SUBJECTS_DIR/bvals.txtset bvecfile = $SUBJECTS_DIR/bvecs.txtset nb0 = 1set doeddy = 1set dorotbvecs = 1set thrbet = 0.3set doregflt = 1set doregbbr = 1set doregmni = 1set mnitemp = Users/Stefano/Desktop/MNI152_T1_1mm_brain.nii.gzset trainfile = $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt# Paths to reconstruct# Default: All pathsset pathlist = (lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \lh.unc_AS rh.unc_AS \fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \lh.cab_PP rh.cab_PP \lh.ccg_PP rh.ccg_PP \lh.slfp_PP rh.slfp_PP \lh.slft_PP rh.slft_PP) # Number of path control points# Default: 5set ncpts = 5 When I run this, I have: [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep -c /Users/Stefano/Desktop/dmrirc_single_subjectINFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_provaINFO: Diffusion root is /Applications/freesurfer/subjects/subject_provaActual FREESURFER_HOME /Applications/freesurfertrac-preproc -c /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/dmrirc.local -log /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.log -cmd /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.cmd#-/Applications/freesurfer/bin/trac-preproc #-#@# Image corrections Mar 29 Gen 2013 00:32:23 CETmri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gzmri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz...TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 0, 0)j_ras = (0, 1, 0)k_ras = (0, 0, 1)writing to /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz...cp /Applications/freesurfer/subjects/subject_prova/bvecs.txt /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecscp: /Applications/freesurfer/subjects/subject_prova/bvecs.txt: No such file or directoryDarwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 I apologize but I need to have your help. Thank you very much, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 28-gen-2013 20.03 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: R: Re: TRACULA Hi Stefano - Type which trac-all to find out where trac-all lives on your computer, then copy the updated version over it. a.y On Mon, 28 Jan 2013, std...@virgilio.it wrote: Thank you very much for you kindness Anastasia. The folder that contains .nii.gz file is correct? I'm looking the recommended trac-all update. Where can I put it? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 28-gen-2013 16.45 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: TRACULA Hi Stefano - The argument of the -c option is a configuration file, not a directory. For more info on trac-all and setting up the configuration file, please see the trac-all wiki page: http://www.freesurfer.net/fswiki/trac-all and tracula tutorials:
Re: [Freesurfer] R: Re: R: Re: R: R: Re: TRACULA
Hi Stefano - The file that you defined as your gradient vector file (set bvecfile = ...) doesn't exist. This file has to exist. Hope this helps, a.y On Tue, 29 Jan 2013, std...@virgilio.it wrote: Hi Anastasia, I have prepared this configuration file: # # Set locations of diffusion DICOMs, diffusion output, FreeSurfer recons # # This file contains commands that will be run by trac-all before an analysis. # It is used to set all parameters needed for the analysis. # # Remove a parameter from your dmrirc file if you want to use the default value. # Parameters that don't have default values must be specified. # # Any other commands that you might want to run before an analysis can be added # to this file. # # Original Author: Anastasia Yendiki # CVS Revision Info: # $Author: ayendiki $ # $Date: 2010/12/15 08:36:00 $ # $Revision: 1.1 $ # # Copyright (C) 2010 # The General Hospital Corporation (Boston, MA). # All rights reserved. # # Distribution, usage and copying of this software is covered under the # terms found in the License Agreement file named 'COPYING' found in the # FreeSurfer source code root directory, and duplicated here: # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense # # General inquiries: freesurfer@nmr.mgh.harvard.edu # # FreeSurfer SUBJECTS_DIR # setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/subject_prova # Output directory where trac-all results will be saved set dtroot = $SUBJECTS_DIR # Subject IDs set subjlist = (Diff01) set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) set dcmroot = $SUBJECTS_DIR set dcmlist = (Diff01/data.nii.gz) set bvalfile = $SUBJECTS_DIR/bvals.txt set bvecfile = $SUBJECTS_DIR/bvecs.txt set nb0 = 1 set doeddy = 1 set dorotbvecs = 1 set thrbet = 0.3 set doregflt = 1 set doregbbr = 1 set doregmni = 1 set mnitemp = Users/Stefano/Desktop/MNI152_T1_1mm_brain.nii.gz set trainfile = $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt # Paths to reconstruct # Default: All paths set pathlist = (lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP) # Number of path control points # Default: 5 set ncpts = 5 When I run this, I have: [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep -c /Users/Stefano/Desktop/dmrirc_single_subject INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/dmrirc.local -log/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.log -cmd/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Mar 29 Gen 2013 00:32:23 CET mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz ... cp /Applications/freesurfer/subjects/subject_prova/bvecs.txt/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti .bvecs cp: /Applications/freesurfer/subjects/subject_prova/bvecs.txt: No such file or directory Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 I apologize but I need to have your help. Thank you very much, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 28-gen-2013 20.03 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: R: Re: TRACULA Hi Stefano - Type which trac-all to find out where trac-all lives on your computer, then copy the updated version over it. a.y On Mon, 28 Jan 2013, std...@virgilio.it wrote: Thank you very much for you kindness Anastasia. The folder that contains .nii.gz file is correct? I'm looking the recommended trac-all update. Where can I put it? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 28-gen-2013 16.45 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: TRACULA Hi Stefano - The
Re: [Freesurfer] nu_estimate_np_and_em error during recon-all
I was able to verify that 'recon-all -s bert -nuintensitycor' works on the windows virtualbox instance of fs5.1. bert is the sample data that comes with the distribution, and nuintensitycor is the stage that runs nu_correct. I noticed in your recon-all.log file this line: total used free Mem: 1026680 673692 352988 which means only 353KB of memory is available for freesurfer. this is way too low. freesurfer needs ideally 4GB, but at least 2GB. make sure when you create the new instance in virtual box that you give it the maximum memory your system allows. this means your windows machine should have at least 4GB, ideally 6-8GB (because windows will take 2GB, and xubuntu will take 1GB). type 'free' in the terminal to get the available memory under the 'free' column. confirm that 'recon-all -s bert -all' runs successfully for you prior to running unknown/new data. Nick On Mon, 2013-01-28 at 19:01 +, Tudor Popescu wrote: Hi Nick, Thanks for your help, I'm on Windows XP SP3 VirtualBox 4.2.4 Tudor On 28 January 2013 18:30, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Tudor, Greg, and Petr, I'm currently attempting to replicate this problem. In the meantime, can you tell me which Windows and which VirtualBox version you are running this on? I'm at a loss as to why this build no longer works. Nick On Mon, 2013-01-28 at 18:19 +, Tudor Popescu wrote: Dear Nick, I was wondering whether you (or indeed anyone else reading this!) know where the error that I report earlier in this thread might be coming from. Many thanks in advance! Tudor On 20 December 2012 05:27, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Tudor, I don't know how to solve this problem. Maybe Nick knows. doug On 12/19/12 6:59 AM, Tudor Popescu wrote: Hi Doug, thanks for replying, here is the file attached. In case the attachment doesn't go through please let me know if I should send it to a different address. Tudor On 18 December 2012 17:34, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you send the recon-all.log file (located in the subject/scripts folder). doug On 12/18/2012 11:41 AM, Tudor Popescu wrote: Hello, First of all, apologies for asking for help three times today! THings will hopefully become clearer once I get used to FS a bit; I really do appreciate the amazing support provided by the team behind FreeSurfer! I ran the following command on one of my structurals: /recon-all -subject M01 -i M01.nii.gz -all/ After a few minutes, recon-all ended with the following message: /Assertion failed at line 827 in file templates/CachedArray.cc/ /nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)/ /nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)/ /ERROR: nu_correct/ /Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux/ I apologise for reporting an error that's already been reported in the past, but unfortunately the solutions suggested in those past threads did not work in my case. To address a few of them: * my PATH (listed
[Freesurfer] Delay
Dear All, I ran a test subject on VM and the process took 20 hrs to complete.But the same images on Mc pro took 58 hours.VM is 8GB and Mpro is 16 GB.I have noticed this delay happening in the past as well,where VM takes 20-24 for a single patient and Mc takes 24-30 for the same.But,this time ,its was so unexpected.Why is this happening?.Which would be more accurate,and does it mean that more time FS take,the better the results? Many thanks Chikku ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
