Hi Nick, So would you recommend I install Centos 6 on the new workstation? In addition, I've run recon-all on a large study group (>100); I take it I'll have to re-run all of them?
Thanks, Chris
-------------------- Chris,
yes, the centos5 build freesurfer 5.1 will work on centos6 (we use it in-house). when the v5.2 release of freesurfer is ready (hopefully at the end of may) you will want to use the centos6 build, as it will get a bit better performance because of the compiler and some openmp options.
n.
On Wed, 2012-04-11 at 10:48 -0400, Chris Watson wrote:
H i Nick, Will the centos5 build of v5.1 work with centos6? I'm getting a new workstation and want to know which version of centos is better to install.
On 04/10/2012 10:08 AM, Nick Schmansky wrote:
Wil,
Hi, the contents of that 'misc' directory is just a filedrop of sorts to supply fixes to individuals who need particular updates. We dont supply formal patches, as it gets too unwieldy to track versions. Rather bug fixes are documented (mostly!) on the ReleaseNotes page with links to fixes.
We have a centos6 build, but dont release it. We will for the next release, v5.2, hopefully by the end of May, as the centos6 build runs a little faster than the centos4/5 build because it uses a newer gcc, but this will mean it wont be possible to mix versions, and a centos6 platform (or kernel 2.6.32-220.7.1.el6.x86_6) will be needed.
mri_info versioning wont affect the stream. i dont think it has any bug fixes outstanding.
i think the trac-all script is the same, the versioning is different because our 'dev' tree version was committed to our 'stable' branch, and the two have different versions (but the file is the same).
n.
Hi-
It would appear the stable release for centos6 is ready for primetime 'stable5.1-bin.tgz'; Is this correct? There is an updated version of 'mri_info' based on file size (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/).
mri_info in 'stable5.1-bin.tgz': 9787048 04-Oct-2011 13:45 mri_info outside of 'stable5.1-bin.tgz': 9866032 04-Oct-2011 11:32
Which version is the most current?
Can the contents of 'stable5.1-bin.tgz' be extracted into /freesurfer/bin to overwrite the extant files?
Additionally, there is a versioning discrepancy between 'trac-all' located in (http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/)
'$Id: trac-all,v 1.35 2011/09/02 19:19:22 ayendiki Exp $'a
and the version packaged with the cenos6_x86_65 'stable5.1-bin.tgz'
'$Id: trac-all,v 1.22.2.9 2011/09/02 19:21:03 ayendiki Exp $'
I did not comprehensively look for any other discrepancies-these just happened to stand out based on the work I was doing today.
Thanks much, Wil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
Chris,
going forward, yes, i would recommend installing centos6. you can use the centos4 freesurfer build in the meantime, until the centos6 freesurfer build (the faster one) is ready. you dont have to rerun your subjects if your happy with the current results. the next release doesnt have any earth-shattering improvements. but if you have on-going subjects that you will need run going forward, then yes, you will need to rerun, because our rule is never to mix results from versions (or in this new case, you cant mix centos4 and centos6 builds of freesurfer).
N.
On Thu, 2012-04-12 at 18:12 +0000, Watson, Christopher wrote:
Hi Nick, So would you recommend I install Centos 6 on the new workstation? In addition, I've run recon-all on a large study group (>100); I take it I'll have to re-run all of them?
Thanks, Chris
Chris,
yes, the centos5 build freesurfer 5.1 will work on centos6 (we use it in-house). when the v5.2 release of freesurfer is ready (hopefully at the end of may) you will want to use the centos6 build, as it will get a bit better performance because of the compiler and some openmp options.
n.
On Wed, 2012-04-11 at 10:48 -0400, Chris Watson wrote:
H i Nick, Will the centos5 build of v5.1 work with centos6? I'm getting a new workstation and want to know which version of centos is better to install.
On 04/10/2012 10:08 AM, Nick Schmansky wrote:
Wil,
Hi, the contents of that 'misc' directory is just a filedrop of sorts to supply fixes to individuals who need particular updates. We dont supply formal patches, as it gets too unwieldy to track versions. Rather bug fixes are documented (mostly!) on the ReleaseNotes page with links to fixes.
We have a centos6 build, but dont release it. We will for the next release, v5.2, hopefully by the end of May, as the centos6 build runs a little faster than the centos4/5 build because it uses a newer gcc, but this will mean it wont be possible to mix versions, and a centos6 platform (or kernel 2.6.32-220.7.1.el6.x86_6) will be needed.
mri_info versioning wont affect the stream. i dont think it has any bug fixes outstanding.
i think the trac-all script is the same, the versioning is different because our 'dev' tree version was committed to our 'stable' branch, and the two have different versions (but the file is the same).
n.
Hi-
It would appear the stable release for centos6 is ready for primetime 'stable5.1-bin.tgz'; Is this correct? There is an updated version of 'mri_info' based on file size (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/).
mri_info in 'stable5.1-bin.tgz': 9787048 04-Oct-2011 13:45 mri_info outside of 'stable5.1-bin.tgz': 9866032 04-Oct-2011 11:32
Which version is the most current?
Can the contents of 'stable5.1-bin.tgz' be extracted into /freesurfer/bin to overwrite the extant files?
Additionally, there is a versioning discrepancy between 'trac-all' located in (http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/)
'$Id: trac-all,v 1.35 2011/09/02 19:19:22 ayendiki Exp $'a
and the version packaged with the cenos6_x86_65 'stable5.1-bin.tgz'
'$Id: trac-all,v 1.22.2.9 2011/09/02 19:21:03 ayendiki Exp $'
I did not comprehensively look for any other discrepancies-these just happened to stand out based on the work I was doing today.
Thanks much, Wil
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@nmr.mgh.harvard.edu
-
Nick Schmansky -
Watson, Christopher