Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Found a fix for that problem: http://www.mathworks.com/matlabcentral/newsreader/view_thread/284776 On Tue, 14 May 2013 14:14:31 -0400 Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Joerg, I'm guessing you have some matlab setup script that has run prior to the freesurfer setup. I see this output: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6 which is not something freesurfer would link against or require. normally it should use /usr/lib64/libstdc++.so.6. try running this prior to sourcing the freesurfer setup: setenv LD_LIBRARY_PATH Glad to see 5.3 works otherwise. Thanks for testing it. Nick On Tue, 2013-05-14 at 15:17 +0200, Joerg Pfannmoeller wrote: Unfortunately encountered a problem in fs-fast stream during execution of selxavg3-sess. Added a relevant part of the log file below: sxa3pwd = /home/...removed... sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./session02 -analysis harm.sm0.mni305 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# session02 ### /home/...removed.../freesurfer_fMRT/session02 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m - outtop = /home/...removed.../freesurfer_fMRT Extension format = nii.gz 1 stim-v-base.mat nruns = 1 autostimdur = outanadir = /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305 Found 45239/537168 ( 8.4) voxels in mask Creating Design Matrix ... creation time = 0.009 sec DoMCFit = 1 ntptot = 100, nX = 8, DOF = 92 Saving X matrix to /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/Xtmp.mat XCond = 444.207 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.493933(t=0.004964) 2 -0.25 -0.269463(t=0.00648) 3 0 -0.0514275(t=0.00734) 4 0.25 0.155364(t=0.008221) 5 0.5 0.337574(t=0.009058) AR1 Correction M: 0.0769642 1.19552 Computing contrast matrices OLS Beta Pass run 1t= 0.0 Global Mean 725.29 Global In-Mask Mean = 725.295 (694.97) Rescale Target = 100 RescaleFactor = 0.137875 OLS Residual Pass run 1t= 0.0 Saving rho1 Smoothing ACF /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer/bin/mri_fwhm) /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /usr/local/freesurfer/bin/mri_fwhm) ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only -- ERROR: fast_selxavg3() failed\n Seemingly a problem with GLIBCXX_3.4.11. My OS is Lubuntu 13.04. On Tue, 14 May 2013 08:28:05 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems. Also freeview runs without an error for the subject bert. On Mon, 13 May 2013 14:40:10 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Just for completeness, I refer to my first contribution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html On Mon, 13 May 2013 13:58:30 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here:
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems. Also freeview runs without an error for the subject bert. On Mon, 13 May 2013 14:40:10 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Just for completeness, I refer to my first contribution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html On Mon, 13 May 2013 13:58:30 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick 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. -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Unfortunately encountered a problem in fs-fast stream during execution of selxavg3-sess. Added a relevant part of the log file below: sxa3pwd = /home/...removed... sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./session02 -analysis harm.sm0.mni305 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# session02 ### /home/...removed.../freesurfer_fMRT/session02 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m - outtop = /home/...removed.../freesurfer_fMRT Extension format = nii.gz 1 stim-v-base.mat nruns = 1 autostimdur = outanadir = /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305 Found 45239/537168 ( 8.4) voxels in mask Creating Design Matrix ... creation time = 0.009 sec DoMCFit = 1 ntptot = 100, nX = 8, DOF = 92 Saving X matrix to /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/Xtmp.mat XCond = 444.207 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.493933(t=0.004964) 2 -0.25 -0.269463(t=0.00648) 3 0 -0.0514275(t=0.00734) 4 0.25 0.155364(t=0.008221) 5 0.5 0.337574(t=0.009058) AR1 Correction M: 0.0769642 1.19552 Computing contrast matrices OLS Beta Pass run 1t= 0.0 Global Mean 725.29 Global In-Mask Mean = 725.295 (694.97) Rescale Target = 100 RescaleFactor = 0.137875 OLS Residual Pass run 1t= 0.0 Saving rho1 Smoothing ACF /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer/bin/mri_fwhm) /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /usr/local/freesurfer/bin/mri_fwhm) ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only -- ERROR: fast_selxavg3() failed\n Seemingly a problem with GLIBCXX_3.4.11. My OS is Lubuntu 13.04. On Tue, 14 May 2013 08:28:05 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems. Also freeview runs without an error for the subject bert. On Mon, 13 May 2013 14:40:10 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Just for completeness, I refer to my first contribution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html On Mon, 13 May 2013 13:58:30 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick 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. -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Joerg, I'm guessing you have some matlab setup script that has run prior to the freesurfer setup. I see this output: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6 which is not something freesurfer would link against or require. normally it should use /usr/lib64/libstdc++.so.6. try running this prior to sourcing the freesurfer setup: setenv LD_LIBRARY_PATH Glad to see 5.3 works otherwise. Thanks for testing it. Nick On Tue, 2013-05-14 at 15:17 +0200, Joerg Pfannmoeller wrote: Unfortunately encountered a problem in fs-fast stream during execution of selxavg3-sess. Added a relevant part of the log file below: sxa3pwd = /home/...removed... sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./session02 -analysis harm.sm0.mni305 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# session02 ### /home/...removed.../freesurfer_fMRT/session02 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m - outtop = /home/...removed.../freesurfer_fMRT Extension format = nii.gz 1 stim-v-base.mat nruns = 1 autostimdur = outanadir = /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305 Found 45239/537168 ( 8.4) voxels in mask Creating Design Matrix ... creation time = 0.009 sec DoMCFit = 1 ntptot = 100, nX = 8, DOF = 92 Saving X matrix to /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/Xtmp.mat XCond = 444.207 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.493933(t=0.004964) 2 -0.25 -0.269463(t=0.00648) 3 0 -0.0514275(t=0.00734) 4 0.25 0.155364(t=0.008221) 5 0.5 0.337574(t=0.009058) AR1 Correction M: 0.0769642 1.19552 Computing contrast matrices OLS Beta Pass run 1t= 0.0 Global Mean 725.29 Global In-Mask Mean = 725.295 (694.97) Rescale Target = 100 RescaleFactor = 0.137875 OLS Residual Pass run 1t= 0.0 Saving rho1 Smoothing ACF /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer/bin/mri_fwhm) /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /usr/local/freesurfer/bin/mri_fwhm) ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only -- ERROR: fast_selxavg3() failed\n Seemingly a problem with GLIBCXX_3.4.11. My OS is Lubuntu 13.04. On Tue, 14 May 2013 08:28:05 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems. Also freeview runs without an error for the subject bert. On Mon, 13 May 2013 14:40:10 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Just for completeness, I refer to my first contribution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html On Mon, 13 May 2013 13:58:30 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Hi, all I have just finnished my FS 5.3-Beta recon-all test in Fedora 18 and compared to FS 5.2 in CentOS6. Both OS are installed in the same machine but different HDs. I used recon-all -all -hippo-subfield in the same subject for both runs and it worked great. The time in both versions were similar: Fedora 18 (FS 5.3 Beta) CentOS6 (FS 5.2 release) Start Tue May 14 02:09:57 2013 Sun April 14 23:45:26 2013 End Tue May 14 14:23:31 2013 Mon April 15 12:50:12 2013 Processing time 12:13:34 13:04:46 As I said in previous post. tksurfer and tkmedit are all Ok. Freeview runs but volumes and surfaces are misaligned. Comparing the results from recon-all, some like volume of the hippocampi subfields and eTIV are identical but other numbers like Brain Segmentation Volume are quite different. I am attaching aseg.stats from both runs. Em Dom, 2013-05-12 às 22:41 -0400, Nick Schmansky escreveu: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick 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. # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /home/marcos/freesurfer/ASegStatsLUT.txt --subject gus # sysname Linux # hostname freesurfer # machine x86_64 # user marcos # anatomy_type volume # # SUBJECTS_DIR /home/marcos/freesurfer/subjects # subjectname gus # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1139453.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1122310.00, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1123071.316664, mm^3 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 262768.814347, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 266640.410169, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 529409.224516, mm^3 # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 211530.623754, mm^3 # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 214452.468393, mm^3 # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 425983.092148, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 63239.00, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 669867.224516, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1033963.316664, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1020057.316664, mm^3 # Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 1017844.00, mm^3 # Measure Mask, MaskVol, Mask Volume, 1501537.00, mm^3 # Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 0.757655, unitless # Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 0.998415, unitless # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 17, unitless # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 17, unitless # Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 34, unitless # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1503920.190724, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2013/04/15 05:59:23 # ColorTable /home/marcos/freesurfer/ASegStatsLUT.txt # ColorTableTimeStamp 2013/02/26 03:23:16 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2013/04/15 00:44:47 # InVolFrame
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick 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. -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Just for completeness, I refer to my first contribution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html On Mon, 13 May 2013 13:58:30 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick 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. -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Hi Nick, I installed it on Ubuntu 13.04 and all tools seem to work. I didn't test recon-all yet. Cheers, Daniel On Sun, May 12, 2013 at 10:41 PM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick ___ 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. -- Daniel Haehn FNNDSC / BCH +1.857.218.5140 ___ 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.
