External Email - Use Caution
Hello Tristan,
I can send you an email directly later today with some tests you can try for
freeview and some other commands If the test succeeds, then at least it
would mean your environment is good.
The original bug report on the Arch Linus page - while listing a signal
11 - did not look to me like it was not from the same cause as what you
subsequently posted. That error was detecting a divide by zero (before it
happened) in the hardware from some calculation which I take to mean the loader
had previously found everything it needed to load the binaries into memory and
run them.
BTW - the 7.1.0 binaries on the download page should work on CentOS8 if you
have that OS to try.
- R.
On May 13, 2020, at 18:09, TRISTAN J PAUTSCH <tpaut...@wisc.edu>
wrote: 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
<tpaut...@wisc.edu>Sent: Friday, April 17, 2020 12:21
PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: ts...@rcmd.org <ts...@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/TFrom: TRISTAN
J PAUTSCH <tpaut...@wisc.edu>Sent: Monday, April 6, 2020 1:32
PMTo: freesurfer@nmr.mgh.harvard.edu
<freesurfer@nmr.mgh.harvard.edu>Cc: ts...@rcmd.org
<ts...@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/vod1t4vlycd9baom42qqqwkc6unj9auiLet me know
how else I can help!TFrom: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard..edu> on behalf of
fsbu...@contbay.com <fsbu...@contbay.com>Sent: Tuesday, March 31,
2020 6:20 PMTo: freesurfer@nmr.mgh.harvard.edu
<freesurfer@nmr.mgh.harvard.edu>Cc: ts...@rcmd.org
<ts...@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 <tpaut...@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.htmlI
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.htmlBack
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?TFrom: fsbu...@contbay.com <fsbu...@contbay.com>Sent: Tuesday,
March 31, 2020 3:57
AMTo: freesur...@nmr.mgh..harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: ts...@rcmd.org <ts...@rcmd.org>;
TRISTAN J PAUTSCH <tpaut...@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/BuildRequirements- R.On Mar 31,
2020, at 02:50, Tim Schäfer <ts...@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
SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent
Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt,
Goethe University Frankfurt am Main, GermanyOn March 30, 2020 at 11:01 PM
TRISTAN J PAUTSCH <tpaut...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of fsbu...@contbay.com
<fsbu...@contbay.com>Sent: Monday, March 30, 2020 9:40 AMTo:
freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc:
dr.minafak...@live.com <dr.minafak...@live.com>Subject: Re: [Freesurfer]
FreeSurfer V 7.0 on Centos 8 External
Email - Use CautionHello 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.minafak...@live.com>
wrote: External Email - Use
CautionGreetings 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 youBest
regardsMina_______________________________________________Freesurfer mailing
listfreesur...@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer
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