On 09/12/2014 11:32 AM, Gurney, Jenny wrote: > Thanks, Zeke. OK, that makes sense about the static vs. dynamic linking > information. Good to know about the usage of UPX in case we need to > 'decompress' at some point and use 'ldd' and get specific library dependency > information. > > The list of binaries/scripts came via the FTP download site here: > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ This is something that I put together and others on the team have not necessarily been contributing to it (not even me on all occasions), so it might not be complete. > > >From the 'Release Notes' page, it looks like the 'official' patches are: > > mri_segstats > mni152reg > recon-all > > Does that sounds right? And (going back to the original question) could we > just overlay these on 5.3.0-HCP with no expected issues? That looks right. Again, I don't know about the HCP release doug > > Thanks, > Matt House, Jenny Gurney and John Flavin @WU in STL > > -----Original Message----- > From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] > Sent: Thursday, September 11, 2014 9:55 AM > To: freesurfer@nmr.mgh.harvard.edu; Gurney, Jenny > Subject: Re: [Freesurfer] FW: Most recent/complete FreeSurfer + Patches? > > Jenny, > > May I ask were you got those list of binaries... Was is from the Release > Notes page? I ask because we link to some "official" patches on the release > notes page but we also frequently give people "dev" versions of some binaries > to help solve a particular issue that they may be having. > Those dev version are not official patches. > > Also, the release version appear statically linked because they get run > through a utility called 'upx' which shrinks them but changes how the 'file' > and 'ld' command process them. The binaries you mention below have not been > run through that utility. > > -Zeke > > On 09/09/2014 01:09 PM, Gurney, Jenny wrote: >> Hi guys! >> >> We would like to install the latest and greatest FreeSurfer on the >> processing cluster used by the CNDA at Washington University. We're >> thinking about installing the 5.3.0-HCP, and then over that, the >> released 5.3.0 patches. We're looking for verification that doing the >> install this way makes sense and that these two code sets don't >> conflict in any way. >> >> We know that the 5.3.0-HCP version updates the mris_make_surfaces, >> however, the patches do not include that update, which is why we are >> thinking about starting with 5.3.0-HCP as the base install. Note that >> this is being done on CentOS 6.x >> >> The currently available patches seem to include: >> >> mni152reg >> >> mri_mcsim >> >> mri_segstats >> >> recon-all >> >> tksurfer-sess >> >> tksurferfv >> >> Is that a complete list or did we miss some binaries/scripts? >> >> Also, it seems that the 'patch' binaries are dynamically linked, while >> the release binaries are statically linked. Besides dependency >> issues, could this cause an issue with results consistency, etc. if >> other system libraries get updated? >> >> Thanks, guys. Hope all is well. >> >> Matt House, Jenny Gurney and John Flavin @WU in STL >> >> >> ---------------------------------------------------------------------- >> -- >> >> The material in this message is private and may contain Protected >> Healthcare Information (PHI). If you are not the intended recipient, >> be advised that any unauthorized use, disclosure, copying or the >> taking of any action in reliance on the contents of this information >> is strictly prohibited. If you have received this email in error, >> please immediately notify the sender via telephone or return 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. > > > ________________________________ > > The material in this message is private and may contain Protected Healthcare > Information (PHI). If you are not the intended recipient, be advised that any > unauthorized use, disclosure, copying or the taking of any action in reliance > on the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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