Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded
Hi, I'm getting a new error mri_tessellate: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory Linux dws-9 3.2.0-4-amd64 #1 SMP Debian 3.2.60-1+deb7u1 x86_64 GNU/Linux For this particular library for Debian, there is *.so.5 and *.so.7. Which should we use? So many thanks for your help on this. Ione ___ 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] mri_tessellate: max vertices 1000000 exceeded
I will have to investigate why this error is occurring as it shouldn't be happening. But regardless a quick fix should be to symlink to the *.so.7 as that is more likely to be backwards compatible: $ cd /usr/lib64 $ sudo ln -s libnetcdf.so.7 libnetcdf.so.6 -Zeke On 07/14/2015 12:59 PM, Ione Fine wrote: Hi, I'm getting a new error mri_tessellate: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory Linux dws-9 3.2.0-4-amd64 #1 SMP Debian 3.2.60-1+deb7u1 x86_64 GNU/Linux For this particular library for Debian, there is *.so.5 and *.so.7. Which should we use? So many thanks for your help on this. Ione ___ 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] mri_tessellate: max vertices 1000000 exceeded
Hello, Here is a download link to the most recent version of mri_tessellate: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_tessellate Please place the new version in your $FREESURFER_HOME/bin directory, and backup the original. Hope this helps. -Zeke FREESURFER_HOME: /usr/local/freesurfer/stable5_3 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: 7.6 Kernel info: Linux 3.2.0-4-amd64 x86_64 I think the info was at the end of the original email, as per instructions. I'm guessing it was just hidden, but let me know if there's any other info you need? Thanks! Ione -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Saturday, July 11, 2015 3:01 PM To: ionef...@uw.edu; Freesurfer support list Subject: Re: [Freesurfer] mri_tessellate: max vertices 100 exceeded Hi Iona if you tell us what your hardware/software environment is we'll get you a newer version. cheers Bruce On Sat, 11 Jul 2015, Ione Fine wrote: Hi, I am running to an error analyzing a 0.5 mm resolution T1 structural with the following with the following: recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT the issue seems to be: mri_tessellate: max vertices 100 exceeded There?s apparently a version of mri_tesselate which is easier going about the number of vertices, but the link to it is broken. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-August/0400 01.html Thanks Ione System information: FREESURFER_HOME: /usr/local/freesurfer/stable5_3 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: 7.6 Kernel info: Linux 3.2.0-4-amd64 x86_64 Professor of Psychology University of Washington http://faculty.washington.edu/ionefine/ ___ 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] mri_tessellate: max vertices 1000000 exceeded
Hi Iona if you tell us what your hardware/software environment is we'll get you a newer version. cheers Bruce On Sat, 11 Jul 2015, Ione Fine wrote: Hi, I am running to an error analyzing a 0.5 mm resolution T1 structural with the following with the following: recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT the issue seems to be: mri_tessellate: max vertices 100 exceeded There’s apparently a version of mri_tesselate which is easier going about the number of vertices, but the link to it is broken. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-August/040001.html Thanks Ione System information: FREESURFER_HOME: /usr/local/freesurfer/stable5_3 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: 7.6 Kernel info: Linux 3.2.0-4-amd64 x86_64 Professor of Psychology University of Washington http://faculty.washington.edu/ionefine/ ___ 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] mri_tessellate: max vertices 1000000 exceeded
I think the info was at the end of the email, as per instructions. Is there any other info you need? Thanks! Ione FREESURFER_HOME: /usr/local/freesurfer/stable5_3 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: 7.6 Kernel info: Linux 3.2.0-4-amd64 x86_64 -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Saturday, July 11, 2015 3:01 PM To: ionef...@uw.edu; Freesurfer support list Subject: Re: [Freesurfer] mri_tessellate: max vertices 100 exceeded Hi Iona if you tell us what your hardware/software environment is we'll get you a newer version. cheers Bruce On Sat, 11 Jul 2015, Ione Fine wrote: Hi, I am running to an error analyzing a 0.5 mm resolution T1 structural with the following with the following: recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT the issue seems to be: mri_tessellate: max vertices 100 exceeded There?s apparently a version of mri_tesselate which is easier going about the number of vertices, but the link to it is broken. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-August/0400 01.html Thanks Ione System information: FREESURFER_HOME: /usr/local/freesurfer/stable5_3 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: 7.6 Kernel info: Linux 3.2.0-4-amd64 x86_64 Professor of Psychology University of Washington http://faculty.washington.edu/ionefine/ ___ 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] mri_tessellate: max vertices 1000000 exceeded
FREESURFER_HOME: /usr/local/freesurfer/stable5_3 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: 7.6 Kernel info: Linux 3.2.0-4-amd64 x86_64 I think the info was at the end of the original email, as per instructions. I'm guessing it was just hidden, but let me know if there's any other info you need? Thanks! Ione -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Saturday, July 11, 2015 3:01 PM To: ionef...@uw.edu; Freesurfer support list Subject: Re: [Freesurfer] mri_tessellate: max vertices 100 exceeded Hi Iona if you tell us what your hardware/software environment is we'll get you a newer version. cheers Bruce On Sat, 11 Jul 2015, Ione Fine wrote: Hi, I am running to an error analyzing a 0.5 mm resolution T1 structural with the following with the following: recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT the issue seems to be: mri_tessellate: max vertices 100 exceeded There?s apparently a version of mri_tesselate which is easier going about the number of vertices, but the link to it is broken. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-August/0400 01.html Thanks Ione System information: FREESURFER_HOME: /usr/local/freesurfer/stable5_3 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: 7.6 Kernel info: Linux 3.2.0-4-amd64 x86_64 Professor of Psychology University of Washington http://faculty.washington.edu/ionefine/ ___ 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] mri_tessellate: max vertices 1000000 exceeded
Hello, The latest version of mri_tessellate can be downloaded using this the following link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_tessellate It would be wise to backup your existing version befor overwriting it with the version contained in the link above. -Zeke On 08/19/2014 05:52 PM, Michiel Kleinnijenhuis wrote: Hi, While doing a high resolution ex vivo recon job, I came across the error mri_tessellate: max vertices 100 exceeded As mentioned in the threads http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35305.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35305.html http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31331.html there seems to be an easy fix. Does anyone have a compiled version of mri_tesselate with the vertex limit relaxed; for Mac (freesurfer-Darwin-lion-stable-pub-v5.3.0)? Thanks! Michiel Kleinnijenhuis == *Michiel Kleinnijenhuis* Postdoctoral researcher FMRIB Centre Nuffield Department of Clinical Neurosciences University of Oxford ___ 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] mri_tessellate: max vertices 1000000 exceeded
Thanks Zeke Bruce On Aug 20, 2014, at 1:55 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Hello, The latest version of mri_tessellate can be downloaded using this the following link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_tessellate It would be wise to backup your existing version befor overwriting it with the version contained in the link above. -Zeke On 08/19/2014 05:52 PM, Michiel Kleinnijenhuis wrote: Hi, While doing a high resolution ex vivo recon job, I came across the error mri_tessellate: max vertices 100 exceeded As mentioned in the threads http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35305.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35305.html http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31331.html there seems to be an easy fix. Does anyone have a compiled version of mri_tesselate with the vertex limit relaxed; for Mac (freesurfer-Darwin-lion-stable-pub-v5.3.0)? Thanks! Michiel Kleinnijenhuis == *Michiel Kleinnijenhuis* Postdoctoral researcher FMRIB Centre Nuffield Department of Clinical Neurosciences University of Oxford ___ 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.
