Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

Re: [Freesurfer] nu_correct error: Can't locate Sys/Hostname.pm in @INC
by fsbuild 09 Apr '25

09 Apr '25

External Email - Use Caution  We are no longer supporting or releasing tar archives for the reasons explained in the previous email. Various sites install freesurfer package(s) on central machine(s)  for everyone to use/mount read only over the network in order to avoid installing and maintaining the same package on 100’s of machines.   However, my understanding is tools like puppet, chef, yum-cron, etc. can if need be automate doing the actual package installs site wide across multiple machines. - R.On Apr 9, 2025, at 15:44, Billah, Tashrif <tbillah(a)bwh.harvard.edu> wrote:I just checked that the only additional step you recommend is: > apt-get install ./freesurfer_ubuntu22-7.4.1_amd64.deb Sourcing the rest have remained the same. So why can you not also upload the tar ball? -TashrifFrom: Billah, Tashrif Sent: Wednesday, April 9, 2025 3:31 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] nu_correct error: Can't locate Sys/Hostname.pm in @INC We have always untarred up to 7.1.0 and used it successfully. This was the good thing about FreeSurfer that did not require a client side installation. I am the administrator and I can tell you that installation of this software via root is infeasible for 100 computers. Given your comment about 7.4.1 tarball being not installer, we want to know--has the installation mechanism changed since 7.4.1? Best,Tashrif_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] nu_correct error: Can't locate Sys/Hostname.pm in @INC
by fsbuild 09 Apr '25

09 Apr '25

External Email - Use Caution  It’s not practical for us to support freesurfer running on a system w/o a successful install via the rpm or deb file freesurfer installers, i.e., the tar archives were not installers.   Use of the installer packages is the standard way to help ensure the files a distribution needs to run are present on the system.  Or the install will fail if the freesurfer requirements conflict with what's currently installed on the system.   If you don't have permission, then please ask someone in your IT/support department to try installing the freesurfer package. - R. On Apr 9, 2025, at 13:56, Billah, Tashrif <tbillah(a)bwh.harvard.edu> wrote:Hi fsbuild, I understand your suggestion about installing version 8. But, can you upload this release as a tar.gz file like you guys have always done for prior releases? Remember that end users will not have root permissions to install an rpm file. Best,Tashrif_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] nu_correct error: Can't locate Sys/Hostname.pm in @INC
by Billah, Tashrif 09 Apr '25

09 Apr '25

Hi fsbuild, I understand your suggestion about installing version 8. But, can you upload this release as a tar.gz file like you guys have always done for prior releases? Remember that end users will not have root permissions to install an rpm file. Best, Tashrif

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Re: [Freesurfer] FreeSurfer 8 on Ubuntu 24.04
by fsbuild 08 Apr '25

08 Apr '25

External Email - Use Caution Please see the recent post,https://secure-web.cisco.com/1KCHTNX-B1zP9SDBeZBUF4EyohuSTVWQnK565FzMy… On Apr 8, 2025, at 13:23, Nagesh Adluru <adluru(a)wisc.edu> wrote:        External Email - Use Caution        Dear FreeSurfer development team, Could you kindly let us know if FreeSurfer 8 native installer for Ubuntu 24.04 would be released sometime in the near future? Thank you so much for the help and guidance. Please let us know if you have any questions or suggestions. Sincerely,Nagesh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] nu_correct error: Can't locate Sys/Hostname.pm in @INC
by fsbuild 08 Apr '25

08 Apr '25

External Email - Use Caution  If your path /software/rocky9/… means you are trying to run a 7.4.1 release on Rocky9 Linux, then I would not expect it to work.  Starting with the 8.0.0 release, there is a Rocky8 installer that I think will also work on Rocky9.   Please see the release page at,https://secure-web.cisco.com/1cdkdm-VjSPKz6eCLzOVZPN9EdLt6weq_jIU-Vi8uL0… - R. On Apr 8, 2025, at 16:49, Billah, Tashrif <tbillah(a)bwh.harvard.edu> wrote:Hi all, In freesurfer-7.4.1, the nu_correct command gives this error: ```Can't locate Sys/Hostname.pm in @INC (you may need to install the Sys::Hostname module) (@INC contains: /software/rocky9/freesurfer-7.4.1/mni/share/perl5 /usr/local/lib64/perl5/5.32 /usr/local/share/perl5/5.32 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/MiscUtilities.pm line 36.BEGIN failed--compilation aborted at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/MiscUtilities.pm line 36.Compilation failed in require at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/Spawn.pm line 35.BEGIN failed--compilation aborted at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/Spawn.pm line 35.Compilation failed in require at /software/rocky9/freesurfer-7.4.1/mni/bin/nu_correct line 38.BEGIN failed--compilation aborted at /software/rocky9/freesurfer-7.4.1/mni/bin/nu_correct line 3``` We are in Redhat 9 OS. Is this expected? Could you recommend a solution? Best,Tashrif_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Search the archives link is not working
by fsbuild 08 Apr '25

08 Apr '25

External Email - Use Caution  I can reach this URL,https://secure-web.cisco.com/1he9MZver8hcuQJFs-vJQC4CflnTxZIHGyJzzULPJv… R. On Apr 8, 2025, at 16:44, Billah, Tashrif <tbillah(a)bwh.harvard.edu> wrote:Hi all, The "search the archives" link, found in FreeSurferSupport webpage, is not working:http://secure-web.cisco.com/1FOB0N8PjWPL99kzHL3Ba-5jNErWhFlNKUPmT8J… Is this expected? Best, Tashrif_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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nu_correct error: Can't locate Sys/Hostname.pm in @INC
by Billah, Tashrif 08 Apr '25

08 Apr '25

Hi all, In freesurfer-7.4.1, the nu_correct command gives this error: ``` Can't locate Sys/Hostname.pm in @INC (you may need to install the Sys::Hostname module) (@INC contains: /software/rocky9/freesurfer-7.4.1/mni/share/perl5 /usr/local/lib64/perl5/5.32 /usr/local/share/perl5/5.32 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/MiscUtilities.pm line 36. BEGIN failed--compilation aborted at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/MiscUtilities.pm line 36. Compilation failed in require at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/Spawn.pm line 35. BEGIN failed--compilation aborted at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/Spawn.pm line 35. Compilation failed in require at /software/rocky9/freesurfer-7.4.1/mni/bin/nu_correct line 38. BEGIN failed--compilation aborted at /software/rocky9/freesurfer-7.4.1/mni/bin/nu_correct line 3 ``` We are in Redhat 9 OS. Is this expected? Could you recommend a solution? Best, Tashrif

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Search the archives link is not working
by Billah, Tashrif 08 Apr '25

08 Apr '25

Hi all, The "search the archives" link, found in FreeSurferSupport webpage, is not working: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ Is this expected? Best, Tashrif

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FreeSurfer 8 on Ubuntu 24.04
by Nagesh Adluru 08 Apr '25

08 Apr '25

External Email - Use Caution Dear FreeSurfer development team, Could you kindly let us know if FreeSurfer 8 native installer for Ubuntu 24.04 would be released sometime in the near future? Thank you so much for the help and guidance. Please let us know if you have any questions or suggestions. Sincerely, Nagesh

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Error using -nonuintensitycor
by Jeffrey Spielberg 07 Apr '25

07 Apr '25

External Email - Use Caution Hello, I'm running Freesurfer 8.0.0 on a Rocky machine and run into an error when I use the -nonuintensitycor flag. The same image finels run perfectly fine without that flag, but with the flag I get this error: #@# Intensity Normalization Tue Mar 18 15:22:23 EDT 2025 /s3l/fs_subjects/RAD_2100A/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... error: mghRead(/s3l/fs_subjects/RAD_2100A/mri/nu.mgz, -1): could not open file^@ error: mri_normalize: could not open source file nu.mgz^@ Command exited with non-zero status 255 This looks to be a bug - any ideas for a workaround? Thanks! -- Jeffrey M. Spielberg, Ph.D. Associate Professor, Clinical Science Department of Psychological and Brain Sciences University of Delaware, Newark, DE 19716 Office: 344 Building X Lab: Suite 302 Building X Email: jmsp(a)udel.edu Web: http://secure-web.cisco.com/1kOZT8vAxRUMrcZR3lkwUFNSIHUk1cRyGyu1QIlfYEHDpjV… Personal Zoom: https://secure-web.cisco.com/1PQ64OpYtuV98rydOWj5-yZN6p9Fy4OUwzLD2N9sfyBBF7… Please be aware that e-mail communication can be intercepted in transmission or misdirected. Please consider communicating any sensitive information by telephone, fax, or mail. The information contained in this message may be privileged and confidential. If you are NOT the intended recipient, please notify the sender immediately and destroy this message.

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