Re: [Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility

[Hoopes, Andrew]

Hi Davide, a centos7 distribution will use the same libraries as a centos6 
distribution. What kind of issues are people reporting? Are there command line 
errors associated with these issues?
Andrew


From:  on behalf of "Vanzo, Davide" 

Reply-To: FS Help 
Date: Tuesday, September 25, 2018 at 4:37 PM
To: FS Help 
Subject: Re: [Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility


External Email - Use Caution
Andrew,

Unfortunately our users have reported issues using freeview.bin in CentOS 7.
The reason being that the CentOS 6 binaries that you provide depend on an 
ancient version of VTK.
Since you provide nightly build for CentOS 7, would it be possible to have a 
CentOS 7 build also for the stable release?

Best regards

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.vanderbilt.edu/accre


On 2018-02-21 10:35:42-06:00 freesurfer-boun...@nmr.mgh.harvard.edu wrote:
Andrew,

Thank you for the confirmation.

Best regards

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
www.accre.vanderbilt.edu


On 2018-02-21 10:23:41-06:00 Hoopes, Andrew wrote:
Hi Davide,
Yes, the centos6 freesurfer6.0 download is compatible with centos7
best
Andrew



On February 20, 2018 at 5:59:04 PM, Vanzo, Davide 
(davide.va...@vanderbilt.edu<mailto:davide.va...@vanderbilt.edu>) wrote:
Hello,

According from few messages in this mailing list, FreeSurfer 6.0.0 should be 
compatible with CentOS 7. However in the official documentation I cannot find 
any related statement. Moveover, the download web page still shows only CentOS 
6 as supported platform.

Could you please clarify if the current stable release works correctly on 
CentOS 7 or not?
Thank you.

Best regards

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
www.accre.vanderbilt.edu
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Re: [Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility

[Vanzo, Davide]

External Email - Use Caution

Andrew,

Unfortunately our users have reported issues using freeview.bin in CentOS 7.
The reason being that the CentOS 6 binaries that you provide depend on an 
ancient version of VTK.
Since you provide nightly build for CentOS 7, would it be possible to have a 
CentOS 7 build also for the stable release?

Best regards

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.vanderbilt.edu/accre


On 2018-02-21 10:35:42-06:00 freesurfer-boun...@nmr.mgh.harvard.edu wrote:

Andrew,

Thank you for the confirmation.

Best regards

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
www.accre.vanderbilt.edu


On 2018-02-21 10:23:41-06:00 Hoopes, Andrew wrote:

Hi Davide,
Yes, the centos6 freesurfer6.0 download is compatible with centos7
best
Andrew



On February 20, 2018 at 5:59:04 PM, Vanzo, Davide 
(davide.va...@vanderbilt.edu) wrote:

Hello,

According from few messages in this mailing list, FreeSurfer 6.0.0 should be 
compatible with CentOS 7. However in the official documentation I cannot find 
any related statement. Moveover, the download web page still shows only CentOS 
6 as supported platform.

Could you please clarify if the current stable release works correctly on 
CentOS 7 or not?
Thank you.

Best regards

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
www.accre.vanderbilt.edu
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Re: [Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility

[Vanzo, Davide]

Andrew,

Thank you for the confirmation.

Best regards

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
www.accre.vanderbilt.edu


On 2018-02-21 10:23:41-06:00 Hoopes, Andrew wrote:

Hi Davide,
Yes, the centos6 freesurfer6.0 download is compatible with centos7
best
Andrew



On February 20, 2018 at 5:59:04 PM, Vanzo, Davide 
(davide.va...@vanderbilt.edu) wrote:

Hello,

According from few messages in this mailing list, FreeSurfer 6.0.0 should be 
compatible with CentOS 7. However in the official documentation I cannot find 
any related statement. Moveover, the download web page still shows only CentOS 
6 as supported platform.

Could you please clarify if the current stable release works correctly on 
CentOS 7 or not?
Thank you.

Best regards

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
www.accre.vanderbilt.edu
___
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility

[Hoopes, Andrew]

Hi Davide,

Yes, the centos6 freesurfer6.0 download is compatible with centos7

best
Andrew



On February 20, 2018 at 5:59:04 PM, Vanzo, Davide 
(davide.va...@vanderbilt.edu) wrote:

Hello,

According from few messages in this mailing list, FreeSurfer 6.0.0 should be 
compatible with CentOS 7. However in the official documentation I cannot find 
any related statement. Moveover, the download web page still shows only CentOS 
6 as supported platform.

Could you please clarify if the current stable release works correctly on 
CentOS 7 or not?
Thank you.

Best regards

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
www.accre.vanderbilt.edu
___
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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[Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility

[Vanzo, Davide]

Hello,

According from few messages in this mailing list, FreeSurfer 6.0.0 should be 
compatible with CentOS 7. However in the official documentation I cannot find 
any related statement. Moveover, the download web page still shows only CentOS 
6 as supported platform.

Could you please clarify if the current stable release works correctly on 
CentOS 7 or not?
Thank you.

Best regards

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
www.accre.vanderbilt.edu
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Re: [Freesurfer] Freesurfer on Centos 7?

[Caspar M. Schwiedrzik]

great, thanks!
caspar


2016-12-09 16:45 GMT-05:00 <zkauf...@nmr.mgh.harvard.edu>:

>
> To get 5.3 working on machines with perl 5.22 or later I will refer you to
> the following thread:
>
>   https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
> edu/msg50383.html
>
> I cant say for sure how many mni scripts will need to point the the older
> version of perl, its probably subjects dependant. But I would think it
> would be 5 or less.
>
> > Thanks for letting me know!
> > What about v5.3?
> > Do I merely need to replace nu_estimate_np_and_em and sharpen_volume, or
> > is
> > there anything else I would need to get it running?
> > Caspar
> >
> >
> > 2016-12-09 16:27 GMT-05:00 <zkauf...@nmr.mgh.harvard.edu>:
> >
> >>
> >> The dev version of freesurfer (and the upcoming v6 release) is
> >> compatible
> >> with Centos7 and also fixes the perl/MNI issue.
> >>
> >>
> >>
> >> > Hi!
> >> > I was wondering whether there is an update from the 2014 thread on
> >> > Freesurfer's compatibility with Centos 7? The old thread is here:
> >> > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
> >> edu/msg38466.html
> >> >
> >> > I have also come across this website mentioning some changes in the
> >> > installation related to Perl and MNI tools:
> >> > http://miconsult.weebly.com/blog/freesurfer-running-on-centos-7
> >> >
> >> > Any insights would be appreciated.
> >> > Thanks, Caspar
> >> > ___
> >> > 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
> >>
> >>
> >> The information in this e-mail is intended only for the person to whom
> >> it
> >> is
> >> addressed. If you believe this e-mail was sent to you in error and the
> >> e-mail
> >> contains patient information, please contact the Partners Compliance
> >> HelpLine at
> >> http://www.partners.org/complianceline . If the e-mail was sent to you
> >> in
> >> error
> >> but does not contain patient information, please contact the sender and
> >> properly
> >> dispose of the e-mail.
> >>
> >>
> >
>
>
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Re: [Freesurfer] Freesurfer on Centos 7?

[zkaufman]

To get 5.3 working on machines with perl 5.22 or later I will refer you to
the following thread:

  https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50383.html

I cant say for sure how many mni scripts will need to point the the older
version of perl, its probably subjects dependant. But I would think it
would be 5 or less.

> Thanks for letting me know!
> What about v5.3?
> Do I merely need to replace nu_estimate_np_and_em and sharpen_volume, or
> is
> there anything else I would need to get it running?
> Caspar
>
>
> 2016-12-09 16:27 GMT-05:00 <zkauf...@nmr.mgh.harvard.edu>:
>
>>
>> The dev version of freesurfer (and the upcoming v6 release) is
>> compatible
>> with Centos7 and also fixes the perl/MNI issue.
>>
>>
>>
>> > Hi!
>> > I was wondering whether there is an update from the 2014 thread on
>> > Freesurfer's compatibility with Centos 7? The old thread is here:
>> > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
>> edu/msg38466.html
>> >
>> > I have also come across this website mentioning some changes in the
>> > installation related to Perl and MNI tools:
>> > http://miconsult.weebly.com/blog/freesurfer-running-on-centos-7
>> >
>> > Any insights would be appreciated.
>> > Thanks, Caspar
>> > ___
>> > 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
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>

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Re: [Freesurfer] Freesurfer on Centos 7?

[Caspar M. Schwiedrzik]

Thanks for letting me know!
What about v5.3?
Do I merely need to replace nu_estimate_np_and_em and sharpen_volume, or is
there anything else I would need to get it running?
Caspar


2016-12-09 16:27 GMT-05:00 <zkauf...@nmr.mgh.harvard.edu>:

>
> The dev version of freesurfer (and the upcoming v6 release) is compatible
> with Centos7 and also fixes the perl/MNI issue.
>
>
>
> > Hi!
> > I was wondering whether there is an update from the 2014 thread on
> > Freesurfer's compatibility with Centos 7? The old thread is here:
> > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
> edu/msg38466.html
> >
> > I have also come across this website mentioning some changes in the
> > installation related to Perl and MNI tools:
> > http://miconsult.weebly.com/blog/freesurfer-running-on-centos-7
> >
> > Any insights would be appreciated.
> > Thanks, Caspar
> > ___
> > 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
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Freesurfer on Centos 7?

[zkaufman]

The dev version of freesurfer (and the upcoming v6 release) is compatible
with Centos7 and also fixes the perl/MNI issue.



> Hi!
> I was wondering whether there is an update from the 2014 thread on
> Freesurfer's compatibility with Centos 7? The old thread is here:
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38466.html
>
> I have also come across this website mentioning some changes in the
> installation related to Perl and MNI tools:
> http://miconsult.weebly.com/blog/freesurfer-running-on-centos-7
>
> Any insights would be appreciated.
> Thanks, Caspar
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Freesurfer on Centos 7?

[Caspar M. Schwiedrzik]

Hi!
I was wondering whether there is an update from the 2014 thread on
Freesurfer's compatibility with Centos 7? The old thread is here:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38466.html

I have also come across this website mentioning some changes in the
installation related to Perl and MNI tools:
http://miconsult.weebly.com/blog/freesurfer-running-on-centos-7

Any insights would be appreciated.
Thanks, Caspar
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