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}

2020-05-14 Thread fsbuild 
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 
CautionJust 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 CautionHello 
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 
CautionThanks 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: [Fr

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 fsbuild 
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 
CautionThanks 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.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 Sent: Tuesday,
 March 31, 2020 3:57 
AMTo: 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.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  
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  
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!TFrom: 
freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbu...@contbay.com 
Sent: Monday, March 30, 2020 9:40 AMTo: 
freesurfer@nmr.mgh.harvard.edu Cc: 
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 th

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

- 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
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinf

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

2020-03-31 Thread fsbuild 
External Email - Use Caution

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
- 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 
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  
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!TFrom: 
freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbu...@contbay.com 
Sent: Monday, March 30, 2020 9:40 AMTo: 
freesurfer@nmr.mgh.harvard.edu Cc: 
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  
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.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer@nmr.mgh.harvard.edu
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