from:"TRISTAN J PAUTSCH"

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

2020-05-14 Thread TRISTAN J PAUTSCH

External Email - Use Caution

Thank you for the reply, I look forward to your email.

Perfectly valid point regarding the AUR post, I must not have read it closely 
enough.

RE: CentOS8, we exclusively use Ubuntu on our lab processing servers 
(compatibility reasons), however I will make time to test our surface files 
against CentOS8 in the near future and report back.

Thank you!
T

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbu...@contbay.com 

Sent: Thursday, May 14, 2020 5:32 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: ts...@rcmd.org 
Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) 
{Disarmed}

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  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 mailto:tpaut...@wisc.edu>>
Sent: Friday, April 17, 2020 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: ts...@rcmd.org<mailto:ts...@rcmd.org> 
mailto: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/

T

____
From: TRISTAN J PAUTSCH 
Sent: Monday, April 6, 2020 1:32 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: 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/vod1t4vlycd9baom42qqqwkc6unj9aui

Let me know how else I can help!
T

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbu...@contbay.com 

Sent: Tuesday, March 31, 2020 6:20 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: 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  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.html<https://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<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 respons

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

2020-05-13 Thread TRISTAN J PAUTSCH

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 
Sent: Friday, April 17, 2020 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: 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/

T

____________
From: TRISTAN J PAUTSCH 
Sent: Monday, April 6, 2020 1:32 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: 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/vod1t4vlycd9baom42qqqwkc6unj9aui

Let me know how else I can help!
T

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbu...@contbay.com 

Sent: Tuesday, March 31, 2020 6:20 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: 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  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.html<https://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: fsbu...@contbay.com<mailto:fsbu...@contbay.com> 
mailto:fsbu...@contbay.com>>
Sent: Tuesday, March 31, 2020 3:57 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: ts...@rcmd.org<mailto:ts...@rcmd.org> 
mailto:ts...@rcmd.org>>; TRISTAN J PAUTSCH 
mailto: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.

Ther

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

2020-04-17 Thread TRISTAN J PAUTSCH

External Email - Use Caution

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 
Sent: Monday, April 6, 2020 1:32 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: 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/vod1t4vlycd9baom42qqqwkc6unj9aui

Let me know how else I can help!
T

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbu...@contbay.com 

Sent: Tuesday, March 31, 2020 6:20 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: 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  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.html<https://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: fsbu...@contbay.com<mailto:fsbu...@contbay.com> 
mailto:fsbu...@contbay.com>>
Sent: Tuesday, March 31, 2020 3:57 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: ts...@rcmd.org<mailto:ts...@rcmd.org> 
mailto:ts...@rcmd.org>>; TRISTAN J PAUTSCH 
mailto: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<https://surfer..nmr.mgh.harvard.edu/fswiki/BuildRequirements>

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

2020-04-06 Thread TRISTAN J PAUTSCH

External Email - Use Caution

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-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbu...@contbay.com 

Sent: Tuesday, March 31, 2020 6:20 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: 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  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.html<https://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: fsbu...@contbay.com<mailto:fsbu...@contbay.com> 
mailto:fsbu...@contbay.com>>
Sent: Tuesday, March 31, 2020 3:57 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: ts...@rcmd.org<mailto:ts...@rcmd.org> 
mailto:ts...@rcmd.org>>; TRISTAN J PAUTSCH 
mailto: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<https://surfer..nmr.mgh.harvard.edu/fswiki/BuildRequirements>

- R.

On Mar 31, 2020, at 02:50, Tim Schäfer  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  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

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

2020-03-31 Thread TRISTAN J PAUTSCH

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:
https://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: fsbu...@contbay.com 
Sent: Tuesday, March 31, 2020 3:57 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: ts...@rcmd.org ; TRISTAN J PAUTSCH 
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.

https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements<https://surfer..nmr.mgh.harvard.edu/fswiki/BuildRequirements>

- R.

On Mar 31, 2020, at 02:50, Tim Schäfer  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  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 
 on behalf of fsbu...@contbay.com 

Sent: Monday, March 30, 2020 9:40 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: dr.minafak...@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  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.edu<mailto:Freesurfer@nmr.mgh.harvard.e

Re: [Freesurfer] FreeSurfer V 7.0 on Centos 8

2020-03-30 Thread TRISTAN J PAUTSCH

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 
 on behalf of fsbu...@contbay.com 

Sent: Monday, March 30, 2020 9:40 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: dr.minafak...@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  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.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

Re: [Freesurfer] freeview crash -- petsc error when opening volume

2019-09-10 Thread TRISTAN J PAUTSCH

External Email - Use Caution

In fact, I think I have narrowed the issue completely down to PETSC, 
irrespective of FreeSurfer/FreeView.

In a Hail Mary attempt, I downloaded the PETSC source code and compiled it from 
scratch; I was going to try and replace the very out of date FreeSurfer version 
(2.3.x) with the latest (3.11.x). It includes a builtin post-compile check 
mechanism for testing the libraries, and wouldn't you know it, I get the exact 
same "signal number 11 SEGV: Segmentation Violation" error when running that 
check as I do with FreeView.

As such, I will take this error to the PETSC mailing list (or whatever else 
might be available), as I'm no longer convinced the issue is directly connected 
to FreeSurfer (which explains why literally everything else in FS still works).

Thank you everyone who replied in an attempt to help out, it is greatly 
appreciated.

Tristan

____________
From: TRISTAN J PAUTSCH 
Sent: Tuesday, September 10, 2019 3:56 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

I'd be willing to try pretty much anything at this point...what would be the 
best way to go about doing this?

Also, what exactly is PETSC? The error seems obviously related to it, and 
Googling the issue brings up many results that aren't even related to 
FreeSurfer, rather PETSC. Does FreeSurfer perhaps contain an old version of 
PETSC?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Tuesday, September 10, 2019 3:46 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume


Hi Tristan,

Would it be possible for you to try building against VTK 8.2 and Qt 5.12.x?

Best,
Ruopeng

On 9/10/19 2:51 PM, TRISTAN J PAUTSCH wrote:

External Email - Use Caution

Thank you for the reply.

Just to clarify, everything builds successfully and there are no errors (that 
I've been able to find) for running 99% of FS commands; I installed all the 
deps listed in the makefile and followed the instructions. As with my first 
message to the list, the only issue I appear to have is when trying to open 
surface files on top of volumes in freeview.

I've attached the requested logs.

Thank you!
Tristan


From: fsbuild <mailto:fsbu...@contbay.com>
Sent: Tuesday, September 10, 2019 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: TRISTAN J PAUTSCH <mailto:tpaut...@wisc.edu>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hello Tristan,

Please check to see that what is listed in the makefile.wiki under the section 
for Ubuntu is installed on your machine.   I would also try building with the 
instructions in the makefile if you have not already done so; that works on my 
Ubuntu 18.04 system, although I am not running the server distribution, e.g., 
type “make -f makefile.wiki help”.   The makefile based build will also save 
logs for the cmake command, build and install pass, so you could send me those 
directly - look for ./freesurfer/{cmake.log, make.log, install.log}

- R.

On Sep 10, 2019, at 13:52, TRISTAN J PAUTSCH 
<mailto:tpaut...@wisc.edu> wrote:

External Email - Use Caution
Thank you so much again for the detailed reply.

I attempted your suggestion, following the instructions from the wiki to a T 
and compiled everything from scratch, and I still get the same PETSC error from 
my first post. To be thorough, I again tested on multiple machines, 
experiencing the same error on each.

I also realized I've never posted the specs of the system on which I've been 
attempting all of this, so in case it's relevant to anyone else, here they are:

OS: Ubuntu 18.04 Server
CPU: 4x Xeon Platinum 8164
RAM: 512GB DDR4 ECC (16x32GB DIMMs)


From: TRISTAN J PAUTSCH mailto:tpaut...@wisc.edu>>
Sent: Thursday, August 29, 2019 10:27 AM
To: fsbuild mailto:fsbu...@contbay.com>>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Thank you for the reply, I will try this when time permits!

Tristan

____________
From: fsbuild <mailto:fsbu...@contbay.com>
Sent: Tuesday, August 27, 2019 4:25 PM
To: TRISTAN J PAUTSCH <mailto:tpaut...@wisc.edu>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hello Tristan,

Please try rebuilding the dev branch on your Ubuntu 18 machine using the 
makefile listed from the wiki,

Re: [Freesurfer] freeview crash -- petsc error when opening volume

2019-09-10 Thread TRISTAN J PAUTSCH

External Email - Use Caution

I'd be willing to try pretty much anything at this point...what would be the 
best way to go about doing this?

Also, what exactly is PETSC? The error seems obviously related to it, and 
Googling the issue brings up many results that aren't even related to 
FreeSurfer, rather PETSC. Does FreeSurfer perhaps contain an old version of 
PETSC?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Tuesday, September 10, 2019 3:46 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume


Hi Tristan,

Would it be possible for you to try building against VTK 8.2 and Qt 5.12.x?

Best,
Ruopeng

On 9/10/19 2:51 PM, TRISTAN J PAUTSCH wrote:

External Email - Use Caution

Thank you for the reply.

Just to clarify, everything builds successfully and there are no errors (that 
I've been able to find) for running 99% of FS commands; I installed all the 
deps listed in the makefile and followed the instructions. As with my first 
message to the list, the only issue I appear to have is when trying to open 
surface files on top of volumes in freeview.

I've attached the requested logs.

Thank you!
Tristan


From: fsbuild <mailto:fsbu...@contbay.com>
Sent: Tuesday, September 10, 2019 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: TRISTAN J PAUTSCH <mailto:tpaut...@wisc.edu>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hello Tristan,

Please check to see that what is listed in the makefile.wiki under the section 
for Ubuntu is installed on your machine.   I would also try building with the 
instructions in the makefile if you have not already done so; that works on my 
Ubuntu 18.04 system, although I am not running the server distribution, e.g., 
type “make -f makefile.wiki help”.   The makefile based build will also save 
logs for the cmake command, build and install pass, so you could send me those 
directly - look for ./freesurfer/{cmake.log, make.log, install.log}

- R.

On Sep 10, 2019, at 13:52, TRISTAN J PAUTSCH 
<mailto:tpaut...@wisc.edu> wrote:

External Email - Use Caution
Thank you so much again for the detailed reply.

I attempted your suggestion, following the instructions from the wiki to a T 
and compiled everything from scratch, and I still get the same PETSC error from 
my first post. To be thorough, I again tested on multiple machines, 
experiencing the same error on each.

I also realized I've never posted the specs of the system on which I've been 
attempting all of this, so in case it's relevant to anyone else, here they are:

OS: Ubuntu 18.04 Server
CPU: 4x Xeon Platinum 8164
RAM: 512GB DDR4 ECC (16x32GB DIMMs)


From: TRISTAN J PAUTSCH mailto:tpaut...@wisc.edu>>
Sent: Thursday, August 29, 2019 10:27 AM
To: fsbuild mailto:fsbu...@contbay.com>>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Thank you for the reply, I will try this when time permits!

Tristan

____
From: fsbuild <mailto:fsbu...@contbay.com>
Sent: Tuesday, August 27, 2019 4:25 PM
To: TRISTAN J PAUTSCH <mailto:tpaut...@wisc.edu>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hello Tristan,

Please try rebuilding the dev branch on your Ubuntu 18 machine using the 
makefile listed from the wiki, (wiki page, 
https://surfer.nmr.mgh.harvard.edu/fswiki/CMake) where the download link to 
makefile is 
https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view?usp=sharing
It should go in the same subdirectory that contains the ./freesurfer tree

There are some comments in there which recommend the following be installed for 
Ubuntu, so please check these are installed before building,

  # sudo apt-get install build-essential
  # sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev
  # sudo apt-get install libblas-dev liblapack-dev
  # sudo apt-get install ocl-icd-opencl-dev
  # sudo apt-get install libxmu-dev libxi-dev
  # sudo apt-get install libopencv-dev
  # Ubuntu 16: sudo apt-get install gcc-4.9 g++-4.9 gfortran-4.9
  # Ubuntu 18: sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8 <
  # sudo apt-get install xorg xorg-dev libx11-dev
  # sudo apt-get install tcl tcl-dev tk tk-dev
  # sudo apt-get install qt5-default qtcreator
  # sudo apt-get install libqt5x11extras5-dev
  # sudo apt-get

Re: [Freesurfer] freeview crash -- petsc error when opening volume

2019-09-10 Thread TRISTAN J PAUTSCH

External Email - Use Caution

Thank you so much again for the detailed reply.

I attempted your suggestion, following the instructions from the wiki to a T 
and compiled everything from scratch, and I still get the same PETSC error from 
my first post. To be thorough, I again tested on multiple machines, 
experiencing the same error on each.

I also realized I've never posted the specs of the system on which I've been 
attempting all of this, so in case it's relevant to anyone else, here they are:

OS: Ubuntu 18.04 Server
CPU: 4x Xeon Platinum 8164
RAM: 512GB DDR4 ECC (16x32GB DIMMs)

____
From: TRISTAN J PAUTSCH 
Sent: Thursday, August 29, 2019 10:27 AM
To: fsbuild 
Cc: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Thank you for the reply, I will try this when time permits!

Tristan


From: fsbuild 
Sent: Tuesday, August 27, 2019 4:25 PM
To: TRISTAN J PAUTSCH 
Cc: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hello Tristan,

Please try rebuilding the dev branch on your Ubuntu 18 machine using the 
makefile listed from the wiki, (wiki page, 
https://surfer.nmr.mgh.harvard.edu/fswiki/CMake) where the download link to 
makefile is 
https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view?usp=sharing
It should go in the same subdirectory that contains the ./freesurfer tree

There are some comments in there which recommend the following be installed for 
Ubuntu, so please check these are installed before building,

  # sudo apt-get install build-essential
  # sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev
  # sudo apt-get install libblas-dev liblapack-dev
  # sudo apt-get install ocl-icd-opencl-dev
  # sudo apt-get install libxmu-dev libxi-dev
  # sudo apt-get install libopencv-dev
  # Ubuntu 16: sudo apt-get install gcc-4.9 g++-4.9 gfortran-4.9
  # Ubuntu 18: sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8 <
  # sudo apt-get install xorg xorg-dev libx11-dev
  # sudo apt-get install tcl tcl-dev tk tk-dev
  # sudo apt-get install qt5-default qtcreator
  # sudo apt-get install libqt5x11extras5-dev
  # sudo apt-get install git-annex
  # sudo apt-get install python3-dev

I’ve attached an archive containing that makefile along with the cmake 
output/build logs from my Ubuntu 18.04 machine so you can see what it looks 
like for me, see cmake_make_install_ubuntu18.tgz

I’ve run all the freeview tutorial commands using the 6.0.0 release on my 
Ubuntu 18.04 machine, but have not been able to reproduce a petsc error so far.

- R.

On Aug 27, 2019, at 11:27, TRISTAN J PAUTSCH  wrote:

External Email - Use Caution
Some final bits of troubleshooting information for future readers, since I'm 
assuming this issue will now get lost in the sauce...I'll probably try 
compiling everything from scratch at some point, but my hopes aren't 
particularly high

I manually compiled the missing libs to get the CentOS7 version of FS-dev 
freeview running on Ubuntu 18, and ultimately the same errors occur. As well, I 
replicated this behavior on a separate Ubuntu 18 machine in the environment, 
this time using a different lab's T1/brainmask/surface files. It would 
definitely seem like there is some sort of hard incompatibility with newer 
versions of freeview and loading surface files on top of volumes in Ubuntu 18.

For what it's worth, it's not evident that any other part of FS has an issue; 
all CLI tools seem to work just fine.

Tristan

____
From: TRISTAN J PAUTSCH mailto:tpaut...@wisc.edu>>
Sent: Friday, August 23, 2019 11:38 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Good morning Ruopeng, thank you for your continued assistance!

Unfortunately, I get the same error using the CentOS6 dev version.. I tried the 
CentOS7 dev version, however this led to a series of library errors, the 
majority of which are unsolvable on Ubuntu 18 without individually compiling 
each necessary library (sym-linking newer libraries does not work).

I wanted to ensure I provide the most details possible, so I also installed FS 
5.3.0 and tested the files...interestingly, they opened just fine, no errors at 
all.

This leads me to believe there is some strange incompatibility between Ubuntu 
18 and the 6.x/dev version of FS (at least when it comes to surface files), 
specifically related to PETSC. Is there anything else I can do to help 
troubleshoot?

Tristan


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Thursday, August 22, 2019 5:00 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] f

Re: [Freesurfer] freeview crash -- petsc error when opening volume

2019-08-29 Thread TRISTAN J PAUTSCH

External Email - Use Caution

Thank you for the reply, I will try this when time permits!

Tristan

From: fsbuild 
Sent: Tuesday, August 27, 2019 4:25 PM
To: TRISTAN J PAUTSCH 
Cc: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hello Tristan,

Please try rebuilding the dev branch on your Ubuntu 18 machine using the 
makefile listed from the wiki, (wiki page, 
https://surfer.nmr.mgh.harvard.edu/fswiki/CMake) where the download link to 
makefile is 
https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view?usp=sharing
It should go in the same subdirectory that contains the ./freesurfer tree

There are some comments in there which recommend the following be installed for 
Ubuntu, so please check these are installed before building,

  # sudo apt-get install build-essential
  # sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev
  # sudo apt-get install libblas-dev liblapack-dev
  # sudo apt-get install ocl-icd-opencl-dev
  # sudo apt-get install libxmu-dev libxi-dev
  # sudo apt-get install libopencv-dev
  # Ubuntu 16: sudo apt-get install gcc-4.9 g++-4.9 gfortran-4.9
  # Ubuntu 18: sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8 <
  # sudo apt-get install xorg xorg-dev libx11-dev
  # sudo apt-get install tcl tcl-dev tk tk-dev
  # sudo apt-get install qt5-default qtcreator
  # sudo apt-get install libqt5x11extras5-dev
  # sudo apt-get install git-annex
  # sudo apt-get install python3-dev

I’ve attached an archive containing that makefile along with the cmake 
output/build logs from my Ubuntu 18.04 machine so you can see what it looks 
like for me, see cmake_make_install_ubuntu18.tgz

I’ve run all the freeview tutorial commands using the 6.0.0 release on my 
Ubuntu 18.04 machine, but have not been able to reproduce a petsc error so far.

- R.

On Aug 27, 2019, at 11:27, TRISTAN J PAUTSCH  wrote:

External Email - Use Caution
Some final bits of troubleshooting information for future readers, since I'm 
assuming this issue will now get lost in the sauce...I'll probably try 
compiling everything from scratch at some point, but my hopes aren't 
particularly high

I manually compiled the missing libs to get the CentOS7 version of FS-dev 
freeview running on Ubuntu 18, and ultimately the same errors occur. As well, I 
replicated this behavior on a separate Ubuntu 18 machine in the environment, 
this time using a different lab's T1/brainmask/surface files. It would 
definitely seem like there is some sort of hard incompatibility with newer 
versions of freeview and loading surface files on top of volumes in Ubuntu 18.

For what it's worth, it's not evident that any other part of FS has an issue; 
all CLI tools seem to work just fine.

Tristan

____________
From: TRISTAN J PAUTSCH mailto:tpaut...@wisc.edu>>
Sent: Friday, August 23, 2019 11:38 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Good morning Ruopeng, thank you for your continued assistance!

Unfortunately, I get the same error using the CentOS6 dev version.. I tried the 
CentOS7 dev version, however this led to a series of library errors, the 
majority of which are unsolvable on Ubuntu 18 without individually compiling 
each necessary library (sym-linking newer libraries does not work).

I wanted to ensure I provide the most details possible, so I also installed FS 
5.3.0 and tested the files...interestingly, they opened just fine, no errors at 
all.

This leads me to believe there is some strange incompatibility between Ubuntu 
18 and the 6.x/dev version of FS (at least when it comes to surface files), 
specifically related to PETSC. Is there anything else I can do to help 
troubleshoot?

Tristan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Thursday, August 22, 2019 5:00 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hi Tristan,

Thanks for the files. I have no problem loading them with the latest dev build 
and stable 6.0 build. I do not have an Ubuntu system, though.

If I’m not mistaken you use dev version of freeview binary along with stable 
6.0 FS binary. Is that correct? Is there any chance you can try installing the 
whole FS dev package?

Ruopeng

On Aug 22, 2019, at 12:20 PM, TRISTAN J PAUTSCH 
mailto:tpaut...@wisc.edu>> wrote:

External Email - Use Caution
Ruopeng,

I've uploaded the files to the FTP drop 
(transfer/incoming/freesurfer_data.tar.gz). The command my user is running 
against these files is:

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

Re: [Freesurfer] freeview crash -- petsc error when opening volume

2019-08-27 Thread TRISTAN J PAUTSCH

External Email - Use Caution

Some final bits of troubleshooting information for future readers, since I'm 
assuming this issue will now get lost in the sauce...I'll probably try 
compiling everything from scratch at some point, but my hopes aren't 
particularly high

I manually compiled the missing libs to get the CentOS7 version of FS-dev 
freeview running on Ubuntu 18, and ultimately the same errors occur. As well, I 
replicated this behavior on a separate Ubuntu 18 machine in the environment, 
this time using a different lab's T1/brainmask/surface files. It would 
definitely seem like there is some sort of hard incompatibility with newer 
versions of freeview and loading surface files on top of volumes in Ubuntu 18.

For what it's worth, it's not evident that any other part of FS has an issue; 
all CLI tools seem to work just fine.

Tristan

____________
From: TRISTAN J PAUTSCH 
Sent: Friday, August 23, 2019 11:38 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Good morning Ruopeng, thank you for your continued assistance!

Unfortunately, I get the same error using the CentOS6 dev version. I tried the 
CentOS7 dev version, however this led to a series of library errors, the 
majority of which are unsolvable on Ubuntu 18 without individually compiling 
each necessary library (sym-linking newer libraries does not work).

I wanted to ensure I provide the most details possible, so I also installed FS 
5.3.0 and tested the files...interestingly, they opened just fine, no errors at 
all.

This leads me to believe there is some strange incompatibility between Ubuntu 
18 and the 6.x/dev version of FS (at least when it comes to surface files), 
specifically related to PETSC. Is there anything else I can do to help 
troubleshoot?

Tristan


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Thursday, August 22, 2019 5:00 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hi Tristan,

Thanks for the files. I have no problem loading them with the latest dev build 
and stable 6.0 build. I do not have an Ubuntu system, though.

If I’m not mistaken you use dev version of freeview binary along with stable 
6.0 FS binary. Is that correct? Is there any chance you can try installing the 
whole FS dev package?

Ruopeng

On Aug 22, 2019, at 12:20 PM, TRISTAN J PAUTSCH 
mailto:tpaut...@wisc.edu>> wrote:

External Email - Use Caution

Ruopeng,

I've uploaded the files to the FTP drop 
(transfer/incoming/freesurfer_data.tar.gz). The command my user is running 
against these files is:

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.

Thank you!
Tristan


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Ruopeng Wang 
mailto:rpw...@nmr.mgh.harvard.edu>>
Sent: Thursday, August 22, 2019 8:16 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hi Tristan,

Would it be possible to send us the files and the command-line you run?

Best,
Ruopeng

On Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH 
mailto:tpaut...@wisc.edu>> wrote:

External Email - Use Caution

Adding more details provided by my user:

The crash only happens when loading surface files, either via the -f flag from 
the CLI or directly through the GUI. Could this be an issue with the surface 
files or the manner in which they are created?


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of TRISTAN J PAUTSCH 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Sent: Tuesday, August 20, 2019 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] freeview crash -- petsc error when opening volume

External Email - Use Caution

Greetings all, I'll try to keep this succinct.

I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I 
used the stable 6.0/CentOS 6 download, in addition to the dev version of 
freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have 
ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview 
launches fine and stays open when launched alone, however attempting to open a

Re: [Freesurfer] freeview crash -- petsc error when opening volume

2019-08-23 Thread TRISTAN J PAUTSCH

External Email - Use Caution

Good morning Ruopeng, thank you for your continued assistance!

Unfortunately, I get the same error using the CentOS6 dev version. I tried the 
CentOS7 dev version, however this led to a series of library errors, the 
majority of which are unsolvable on Ubuntu 18 without individually compiling 
each necessary library (sym-linking newer libraries does not work).

I wanted to ensure I provide the most details possible, so I also installed FS 
5.3.0 and tested the files...interestingly, they opened just fine, no errors at 
all.

This leads me to believe there is some strange incompatibility between Ubuntu 
18 and the 6.x/dev version of FS (at least when it comes to surface files), 
specifically related to PETSC. Is there anything else I can do to help 
troubleshoot?

Tristan


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Thursday, August 22, 2019 5:00 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hi Tristan,

Thanks for the files. I have no problem loading them with the latest dev build 
and stable 6.0 build. I do not have an Ubuntu system, though.

If I’m not mistaken you use dev version of freeview binary along with stable 
6.0 FS binary. Is that correct? Is there any chance you can try installing the 
whole FS dev package?

Ruopeng

On Aug 22, 2019, at 12:20 PM, TRISTAN J PAUTSCH 
mailto:tpaut...@wisc.edu>> wrote:

External Email - Use Caution

Ruopeng,

I've uploaded the files to the FTP drop 
(transfer/incoming/freesurfer_data.tar.gz). The command my user is running 
against these files is:

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.

Thank you!
Tristan


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Ruopeng Wang 
mailto:rpw...@nmr.mgh.harvard.edu>>
Sent: Thursday, August 22, 2019 8:16 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hi Tristan,

Would it be possible to send us the files and the command-line you run?

Best,
Ruopeng

On Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH 
mailto:tpaut...@wisc.edu>> wrote:

External Email - Use Caution

Adding more details provided by my user:

The crash only happens when loading surface files, either via the -f flag from 
the CLI or directly through the GUI. Could this be an issue with the surface 
files or the manner in which they are created?


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of TRISTAN J PAUTSCH 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Sent: Tuesday, August 20, 2019 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] freeview crash -- petsc error when opening volume

External Email - Use Caution

Greetings all, I'll try to keep this succinct.

I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I 
used the stable 6.0/CentOS 6 download, in addition to the dev version of 
freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have 
ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview 
launches fine and stays open when launched alone, however attempting to open a 
volume (either through the GUI or directly via the CLI) causes a crash and the 
following error about 5-8 seconds after launching (brain images begin to 
populate, then crash):

---

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org<http://valgrind.org/> on linux or man 
libgmalloc on Apple to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:

Re: [Freesurfer] freeview crash -- petsc error when opening volume

2019-08-22 Thread TRISTAN J PAUTSCH

External Email - Use Caution

Ruopeng,

I've uploaded the files to the FTP drop 
(transfer/incoming/freesurfer_data.tar.gz). The command my user is running 
against these files is:

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.

Thank you!
Tristan


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Thursday, August 22, 2019 8:16 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hi Tristan,

Would it be possible to send us the files and the command-line you run?

Best,
Ruopeng

On Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH 
mailto:tpaut...@wisc.edu>> wrote:

External Email - Use Caution

Adding more details provided by my user:

The crash only happens when loading surface files, either via the -f flag from 
the CLI or directly through the GUI. Could this be an issue with the surface 
files or the manner in which they are created?


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of TRISTAN J PAUTSCH 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Sent: Tuesday, August 20, 2019 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] freeview crash -- petsc error when opening volume

External Email - Use Caution

Greetings all, I'll try to keep this succinct.

I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I 
used the stable 6.0/CentOS 6 download, in addition to the dev version of 
freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have 
ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview 
launches fine and stays open when launched alone, however attempting to open a 
volume (either through the GUI or directly via the CLI) causes a crash and the 
following error about 5-8 seconds after launching (brain images begin to 
populate, then crash):

---

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named xxx by xxx Tue Aug 20 
13:44:15 2019
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)

---

I've seen a number of other posts on the mailing list about this, but all of 
them I could find either end abruptly without a solution or with an unanswered 
request for more info.

Happy to provide any additional information or anything that may aid in the 
resolution of this issue.

Thanks everyone,
~T
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harv

Re: [Freesurfer] freeview crash -- petsc error when opening volume

2019-08-22 Thread TRISTAN J PAUTSCH

External Email - Use Caution

Absolutely, Ruopeng, happy to provide. Would the best avenue for sharing these 
files be the FTP drop (into transfer/incoming) or some other avenue?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Thursday, August 22, 2019 8:16 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hi Tristan,

Would it be possible to send us the files and the command-line you run?

Best,
Ruopeng

On Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH 
mailto:tpaut...@wisc.edu>> wrote:

External Email - Use Caution

Adding more details provided by my user:

The crash only happens when loading surface files, either via the -f flag from 
the CLI or directly through the GUI. Could this be an issue with the surface 
files or the manner in which they are created?


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of TRISTAN J PAUTSCH 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Sent: Tuesday, August 20, 2019 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] freeview crash -- petsc error when opening volume

External Email - Use Caution

Greetings all, I'll try to keep this succinct.

I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I 
used the stable 6.0/CentOS 6 download, in addition to the dev version of 
freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have 
ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview 
launches fine and stays open when launched alone, however attempting to open a 
volume (either through the GUI or directly via the CLI) causes a crash and the 
following error about 5-8 seconds after launching (brain images begin to 
populate, then crash):

---

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named xxx by xxx Tue Aug 20 
13:44:15 2019
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)

---

I've seen a number of other posts on the mailing list about this, but all of 
them I could find either end abruptly without a solution or with an unanswered 
request for more info.

Happy to provide any additional information or anything that may aid in the 
resolution of this issue.

Thanks everyone,
~T
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto: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

Re: [Freesurfer] freeview crash -- petsc error when opening volume

2019-08-21 Thread TRISTAN J PAUTSCH

External Email - Use Caution

Adding more details provided by my user:

The crash only happens when loading surface files, either via the -f flag from 
the CLI or directly through the GUI. Could this be an issue with the surface 
files or the manner in which they are created?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of TRISTAN J PAUTSCH 

Sent: Tuesday, August 20, 2019 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] freeview crash -- petsc error when opening volume


External Email - Use Caution

Greetings all, I'll try to keep this succinct.

I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I 
used the stable 6.0/CentOS 6 download, in addition to the dev version of 
freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have 
ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview 
launches fine and stays open when launched alone, however attempting to open a 
volume (either through the GUI or directly via the CLI) causes a crash and the 
following error about 5-8 seconds after launching (brain images begin to 
populate, then crash):

---

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named xxx by xxx Tue Aug 20 
13:44:15 2019
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)

---

I've seen a number of other posts on the mailing list about this, but all of 
them I could find either end abruptly without a solution or with an unanswered 
request for more info.

Happy to provide any additional information or anything that may aid in the 
resolution of this issue.

Thanks everyone,
~T
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] freeview crash -- petsc error when opening volume

2019-08-20 Thread TRISTAN J PAUTSCH

External Email - Use Caution

Greetings all, I'll try to keep this succinct.

I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I 
used the stable 6.0/CentOS 6 download, in addition to the dev version of 
freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have 
ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview 
launches fine and stays open when launched alone, however attempting to open a 
volume (either through the GUI or directly via the CLI) causes a crash and the 
following error about 5-8 seconds after launching (brain images begin to 
populate, then crash):

---

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named xxx by xxx Tue Aug 20 
13:44:15 2019
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)

---

I've seen a number of other posts on the mailing list about this, but all of 
them I could find either end abruptly without a solution or with an unanswered 
request for more info.

Happy to provide any additional information or anything that may aid in the 
resolution of this issue.

Thanks everyone,
~T
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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

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

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

Re: [Freesurfer] FreeSurfer V 7.0 on Centos 8

Re: [Freesurfer] freeview crash -- petsc error when opening volume

Re: [Freesurfer] freeview crash -- petsc error when opening volume

Re: [Freesurfer] freeview crash -- petsc error when opening volume

Re: [Freesurfer] freeview crash -- petsc error when opening volume

Re: [Freesurfer] freeview crash -- petsc error when opening volume

Re: [Freesurfer] freeview crash -- petsc error when opening volume

Re: [Freesurfer] freeview crash -- petsc error when opening volume

Re: [Freesurfer] freeview crash -- petsc error when opening volume

Re: [Freesurfer] freeview crash -- petsc error when opening volume

[Freesurfer] freeview crash -- petsc error when opening volume

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