[Freesurfer] Problem running recon-all in newly installed Ubuntu 16.04LTS
Hello freesurfer experts, I've recently set up a PC running Ubuntu 16.04LTS and tried to run a freesurfer version which was running well on another PC (also running Ubuntu 16.04LTS)...the nightly build for centos6 of 2016-09-03. I'm running the recon-all script. While running mri_ca_register, I get >> label assignment complete, 7 changed (0.00%) det(m_affine) = 1.19 (predicted orig area = 6.7) label assignment complete, 8 changed (0.00%) Segmentation fault (core dumped) ERROR: mri_ca_register with non-zero status 139 but continuing despite the error >> and a little bit later the program exits. Comparing the recon-all.log files from the runs in the two PCs, they appear identical until the above error appears, with the exception of the "main basin size", where the problematic PC gives a value which is 3.5% of that in the "good" PC. Any idea what may be going wrong with the new PC? Many thanks, Nasos ___ 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] Problem running recon-all in newly installed Ubuntu 16.04LTS
Hi Bruce, Many thanks. The PC has nominally 8Gb of RAM. The recon-all.log gives the following totalusedfree shared buff/cache available Mem:8142944 1081848 6041324 44260 1019772 6725212 Swap: 8353788 0 8353788 Can the problem be that it's only 6.6Gb available? Nikos On 07/12/2016 16:32, Bruce Fischl wrote: > Hi Nasos > > how much RAM is on your new PC? > > cheers > Bruce > On Wed, 7 Dec 2016, Nasos Petridis wrote: > >> Hello freesurfer experts, >> >> I've recently set up a PC running Ubuntu 16.04LTS and tried to run a >> freesurfer version which was running well on another PC (also running >> Ubuntu 16.04LTS)...the nightly build for centos6 of 2016-09-03. I'm >> running the recon-all script. While running mri_ca_register, I get >> >> label assignment complete, 7 changed (0.00%) >> det(m_affine) = 1.19 (predicted orig area = 6.7) >> label assignment complete, 8 changed (0.00%) >> Segmentation fault (core dumped) >> ERROR: mri_ca_register with non-zero status 139 >> but continuing despite the error >> and a little bit later the program exits. >> >> Comparing the recon-all.log files from the runs in the two PCs, they >> appear identical until the above error appears, with the exception of >> the "main basin size", where the problematic PC gives a value which is >> 3.5% of that in the "good" PC. >> >> Any idea what may be going wrong with the new PC? >> >> Many thanks, >> >> Nasos >> ___ >> 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. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: Exporting TIFF and rotating volume with tkmedit in Ubuntu 14.04
Hello, Recently, I started using freesurfer on a Ubuntu system. I've noticed two issues, when using tkmedit, for example: tkmedit subj_name norm.mgz -segmentation aparc.a2009s+aseg.mgz (i) When I try to save TIFF (Tools > Save TIFF), a TIFF file is created, and it can be opened in any image viewing program but is black. It's worth noting that when I try to save a cortical thickness surface view as tiff, using tksurfer tools, it works fine. (ii) When I try to rotate the volume (Tools > Volume > Rotate Volume), I cannot enter an angle in the "Degrees" dialogue box, ie I type the number but no number appears neither doe the cursor move. I've tried both freesurfer 5.3 Linux distributions (centos4, centos6) with no difference. I'm running Ubuntu 14.04LTS. Do I need to install any packages in Ubuntu? Any suggestion how to tackle those two issues would be greatly appreciated. Many thanks, Nasos ___ 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.
