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/

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?

Thanks, Matt House, Jenny Gurney and John Flavin @WU in STL

-----Original Message----- From: Z K [mailto:zkaufman@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

---

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Hello,

Yeah I would ignore the contents of that ftp site and simply go with whatever the contents are on the Release Notes page. The 3 files you have listed make sense based on my quick glance of that page.

And yes, I would simply overlay those files on top of the originals. Although it may be a good idea to back up the originals.

-Zeke

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/

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?

Thanks, Matt House, Jenny Gurney and John Flavin @WU in STL

-----Original Message----- From: Z K [mailto:zkaufman@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

---

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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.

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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.