Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}

External Email - Use Caution

Just following up to confirm that this issue persists in 7.1.0 in case anyone has any ideas; I've tried everything I can think of at this point.

:(

________________________________ From: TRISTAN J PAUTSCH tpautsch@wisc.edu Sent: Friday, April 17, 2020 12:21 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: ts+ml@rcmd.org ts+ml@rcmd.org Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}

Just a quick follow up, I've now been able to find my issue in the wild as well (not just on my own machines).

I use Arch Linux personally and on a small handful of workstations professionally, and when investigating using FS on Arch, I stumbled upon an AUR build someone had done. While I didn't intend to use this buildfile (still version 6.x), the top comment on the below link alludes to the same PETSC error message with FS as I'm experiencing on my Ubuntu machines:

https://aur.archlinux.org/packages/freesurfer-bin/

T

________________________________ From: TRISTAN J PAUTSCH tpautsch@wisc.edu Sent: Monday, April 6, 2020 1:32 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: ts+ml@rcmd.org ts+ml@rcmd.org Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}

Apologies for the late reply, hectic times.

Please find the requested files here: https://uwmadison.box.com/s/vod1t4vlycd9baom42qqqwkc6unj9aui

Let me know how else I can help! T

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fsbuild@contbay.com fsbuild@contbay.com Sent: Tuesday, March 31, 2020 6:20 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: ts+ml@rcmd.org ts+ml@rcmd.org Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}

External Email - Use Caution

Hello Tristan,

Going back to that thread, I’d like to try the command you uploaded data for as freesurfer_data.tar.gz on a couple of Ubuntu systems, but either I’m looking in the wrong place or it’s not there anymore. Is there a shared google drive link or something you point me to for a download link?

freeview -v brainmask.mgz T1.mgz -f lh.white:edgecolor=yellow lh.pial:edgecolor=magenta rh.white:edgecolor=yellow rh.pial:edgecolor=magenta

We can also replicate the error by opening freeview and opening all the above files sequentially through the GUI.

- R.

On Mar 31, 2020, at 13:41, TRISTAN J PAUTSCH tpautsch@wisc.edu wrote:

External Email - Use Caution Thanks for the reply, all.

The issues I'm having are the same as they were in my prior thread, found here: MailScanner has detected a possible fraud attempt from "www..mail-archive.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63458.htmlhttps://www..mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63458.html

I tried everything up to and including compiling everything from scratch (including FS itself, missing libs, PETSC, etc.). The main takeaway is that I pretty convincingly narrowed the issue down to PETSC+Ubuntu 18.04, the most pertinent details for that being in the following post: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63702.html

Back when I was active in that thread, I emailed the PETSC mailing list and got no response, and at the time I was pretty busy with other projects so I had to let it go for the time being; I maintained my old RHEL6 server so people could continue to use FS. Now with everyone in quarantine (and RHEL6 entering ELS this November), it's a decent time to look back into this issue.

I wouldn't have reached back out to the FS list, however when I saw that a focus was being placed on Ubuntu (and that there was a working Ubuntu VM), I became hopeful that maybe this issue was resolved?

T ________________________________ From: fsbuild@contbay.commailto:fsbuild@contbay.com <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: Tuesday, March 31, 2020 3:57 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: ts+ml@rcmd.orgmailto:ts+ml@rcmd.org <ts+ml@rcmd.orgmailto:ts+ml@rcmd.org>; TRISTAN J PAUTSCH <tpautsch@wisc.edumailto:tpautsch@wisc.edu> Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8)

We would also like to know about any issues you are seeing on Ubuntu.

I think Ubuntu eliminated some jpeg/png packages from their repos. Those can be downloaded and installed manually,e.g., libpng12-0_1.2.54-1ubuntu1.1_amd64.deb, libjpeg62_6b2-3_amd64.deb. That is part of the reason we made an Ubuntu 18 VM available with everything pre-installed.

The VM is essentially what has been used for the freesurfer course which runs mostly freeview commands with some mri* commands (though I believe a recon-all also works). The VM is running binaries built on CentOS7 - as the reference platforms for freesurfer dev are currently CentOS and MacOS. We are looking at making a .deb installer for freesurfer on Ubuntu though.

There is some info on the wiki about packages required to compile the source on Ubuntu - but you don’t need all of these to run (even the CentOS) binaries.

MailScanner has detected a possible fraud attempt from "surfer..nmr.mgh.harvard.edu" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirementshttps://surfer..nmr.mgh.harvard.edu/fswiki/BuildRequirements

- R.

On Mar 31, 2020, at 02:50, Tim Schäfer ts+ml@rcmd.org wrote:

External Email - Use Caution

Hi Tristan,

I'm about to setup a FreeSurfer installation on an Ubuntu system, and I wondered whether you could elaborate on the kind of issues you are experiencing.

Best,

Tim

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

On March 30, 2020 at 11:01 PM TRISTAN J PAUTSCH tpautsch@wisc.edu wrote:

External Email - Use Caution

Is there going to be an "official" Ubuntu build this time around (as in, built and tested in Ubuntu) that isn't the VM? Both the current CentOS and the dev builds continue to have issues (even when compiled from scratch) on my Ubuntu 18.04 servers.

Thanks! T

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fsbuild@contbay.com fsbuild@contbay.com Sent: Monday, March 30, 2020 9:40 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: dr.minafakhry@live.com dr.minafakhry@live.com Subject: Re: [Freesurfer] FreeSurfer V 7.0 on Centos 8

External Email - Use Caution

Hello Mina,

I see from https://www.centosblog.com/centos-eol-dates/ that CentOS 6 will no longer be updated as of 11/2020, and similarly for CentOS 7 in 6/2024. It looks like CentOS 8 was released around September of 2019.

While we do not currently build/test on CentOS8, I am sure it will eventually be supported. Given some users will continue to use CentOS 6 even after 11/2020 and that many people have been running the freesurfer 6 release on CentOS6, then even the upcoming freesurfer 7 release is targeting CentOS6, CentOS7 and Ubuntu linux (as well as Mac OS).

There is also currently an Ubuntu 18 VM with freesurfer 6 and the beta release of freesurfer 7 pre-installed which you can find here, https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67

- R.

On Mar 30, 2020, at 08:52, Mina Rizkallah dr.minafakhry@live.com wrote:

External Email - Use Caution Greetings FreeSurfer team,

I recently upgraded by workstation from Centos 7 to 8.1 as the support for centos 7 will be over soon.

I tried installing freesurfer version 7.0 beta 1 but failed due to some unresolved dependencies (tried on a virtual centos 7 and worked fine) !!

so, when will there be support for centos 8, thank you

Best regards Mina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer