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Hi Andrew We are running Ubuntu 19.10 on our computer and as for Freesurfer were we tried to run this on freesurfer 7 and the development version but both produced this error. (freesurfer 7: freesurfer-linux-centos7_ x86_64-7.1.0-20200511-813297 Freesurfer DEV: freesurfer-linux-centos8_ x86_64-dev-20201109-2e16dca)

-Mackenzie

On Wed, Feb 3, 2021 at 10:37 AM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

Hi Mackenzie,

Can you let us know what OS and version you’re running this on?

Thanks,

Andrew

*From: *freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Langan, Mackenzie < mackenzie.langan@icahn.mssm.edu> *Date: *Wednesday, February 3, 2021 at 10:31 AM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Issue with the hypothalamic segmentation

•    External Email - Use Caution        *
  
  

Good Morning,

I have been trying to run the hypothalamic segmentation and get the following error:

*aalqadi@athena:/zstore/data/aalqadi/aalqadi/mPFC/data$ mri_segment_hypothalamic_subunits --s S05486*

*Traceback (most recent call last):*

• File

"/usr/local/freesurfer_dev/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 10, in <module>*

• import freesurfer as fs*

• File

"/usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/__init__.py", line 8, in <module>*

• from . import bindings*

*ImportError: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not found (required by /usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/* *bindings.cpython-36m-x86_64-linux-gnu.so* http://secure-web.cisco.com/1hzKok6ieorAQWILbwXrHm4nWv5aGVWrgLXUjICNL0HcYQDptT0fNHU6AOnJE3qXzhl9NRtNMMllRlwPcgtVISVPA9DsJir2pbwpc4pB0rKgOo_wc0yoGtFyiaXPXPRResPg1pGzrgr4u8Ao1pz7izacK37z0ZG3aoldmpUuq7kUqK3wyc40aHRkJp7A41zrUm-ikFytp9N0shHTbuPDQfnmsIvxVlN5ohXYytZXde24kCCukWp5zEZbAtWoVD6A8g0X2TtrYVzai92-jQmruSg/http%3A%2F%2Fbindings.cpython-36m-x86_64-linux-gnu.so%2F *)*

We installed the development version of freesurfer to see if that would work to run this, but that didn't work. We then installed XCRYPT_2.0 but still got the same error. We have two versions of python on our machine which we amended to fix the problem, but still get the same error. I am at a loss as to what I should try next to implement this. Any help would be great. Thanks

Best,

Mackenzie _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/19hlZ_7axUn8AdTxkDXxN0gm31q3caM72TmC2x6KVSreK-I...

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Yes, so I tried both installing missing libraries and removing some outdated ones to no effect.

This was the result of mri_convert --help: mri_convert:

mri_convert: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not found (required by mri_convert)

On Feb 3, 2021, at 1:04 PM, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

Thanks. Can you run something like `mri_convert --help` to check if this is an issue with all the FS binaries? It seems like this is a known ubuntu bug:

https://secure-web.cisco.com/1N8E40WL9mZXBMl1iywE813eOvqmsKD4hy3ivF4QP8KsEH1... https://secure-web.cisco.com/1DcFyqPO2QclKQ7V8MFZBIYqEx5FJbKfFCxwEcv9lOEgUbb...

It might require updating some libraries on your end, but it’d be nice to see if this is a global issue first. Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Langan, Mackenzie mackenzie.langan@icahn.mssm.edu Date: Wednesday, February 3, 2021 at 11:46 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Issue with the hypothalamic segmentation

    External Email - Use Caution        

Hi Andrew We are running Ubuntu 19.10 on our computer and as for Freesurfer were we tried to run this on freesurfer 7 and the development version but both produced this error. (freesurfer 7: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297 Freesurfer DEV: freesurfer-linux-centos8_x86_64-dev-20201109-2e16dca)

-Mackenzie

On Wed, Feb 3, 2021 at 10:37 AM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote: Hi Mackenzie,

Can you let us know what OS and version you’re running this on?

Thanks, Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Langan, Mackenzie mackenzie.langan@icahn.mssm.edu Date: Wednesday, February 3, 2021 at 10:31 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Issue with the hypothalamic segmentation

    External Email - Use Caution        

Good Morning,

I have been trying to run the hypothalamic segmentation and get the following error:

aalqadi@athena:/zstore/data/aalqadi/aalqadi/mPFC/data$ mri_segment_hypothalamic_subunits --s S05486 Traceback (most recent call last): File "/usr/local/freesurfer_dev/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 10, in <module> import freesurfer as fs File "/usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/__init__.py", line 8, in <module> from . import bindings ImportError: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not found (required by /usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/bindings.cpython-36m-x86_64-linux-gnu.so)

We installed the development version of freesurfer to see if that would work to run this, but that didn't work. We then installed XCRYPT_2.0 but still got the same error. We have two versions of python on our machine which we amended to fix the problem, but still get the same error. I am at a loss as to what I should try next to implement this. Any help would be great. Thanks

Best, Mackenzie _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1CBn87afQucyVqkb-eNYzIybsHcLEf11vRBnVTB7I6RlJDH... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1CBn87afQucyVqkb-eNYzIybsHcLEf11vRBnVTB7I6RlJDH...

Honestly, I’m not really sure how to fix this. This isn’t reproducible, and it appears to be an issue with your system libraries. I don’t know how much we can do about it on our side. Have you reached out to your sys admin, and do you observe this issue elsewhere? It seems like this is commonly observed when running perl as well. Rob, any ideas?

Here is the Debian bug report: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=951880

Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mackenzie Langan mackenzie.langan@icahn.mssm.edu Date: Friday, February 5, 2021 at 9:35 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Issue with the hypothalamic segmentation

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On Feb 3, 2021, at 1:14 PM, Mackenzie Langan mackenzie.langan@icahn.mssm.edu wrote:

Yes, so I tried both installing missing libraries and removing some outdated ones to no effect.

This was the result of mri_convert --help: mri_convert:

mri_convert: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not found (required by mri_convert)

On Feb 3, 2021, at 1:04 PM, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote: Thanks. Can you run something like `mri_convert --help` to check if this is an issue with all the FS binaries? It seems like this is a known ubuntu bug:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://ubuntuforums.org/showthread.php?t=2438576https://secure-web.cisco.com/1EEQYsHuLSmuHK07k0q90qymHo8_e1c-uc0erfhedd7Tc7qLT6kDUz-dxPo7Rce_PIHAmHSF7u4KUQU2X3cAY5lu7d2WDDYS1qFnfSO7JcDrr4JubBL7Zg9OOE4GKnC3aMc7M8yhOE7gXoUiZxtHBWhqpOJeL2w6uAPJ0etBovLXjaa6wFhtAdlYKEp-DJQRSOfRJoW-TvVcZkK_a0BINTKDEAVuqb0oiMR12BWpLgxqko3d3le6lBdNu2VnT3vrXcXGAuMTEXYCN0QBZTpzgiw/https%3A%2F%2Fubuntuforums.org%2Fshowthread.php%3Ft%3D2438576 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://askubuntu.com/questions/1254845/upgrade-from-19-10-to-20-04-failshttps://secure-web.cisco.com/1Kg6s6YYtcmG6yo2nNy72n8QrhfAtozluBCAdoyrEvjTBz5qAZ6XIHd3fRL8BRCQDx39OkxHKjdjCAl-qvHnzEwlZjASQUSWddBIJLaFLlqJ4Sz7_kQw25zed9faPXbMYRCnBc1h1EAlw9w3MeN-7_E-bCHSY_bpWywhyBaRCixtLinsX5T8_i2obEU7tXMhNvoUTA_0pVh3mhCdATJA1GgXhd3hb6m7s7U039vR4TX4crDkLikd4jYFzDxa3w0VaXKI_5IUjp21MENlSOmM2SQ/https%3A%2F%2Faskubuntu.com%2Fquestions%2F1254845%2Fupgrade-from-19-10-to-20-04-fails

It might require updating some libraries on your end, but it’d be nice to see if this is a global issue first. Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Langan, Mackenzie mackenzie.langan@icahn.mssm.edu Date: Wednesday, February 3, 2021 at 11:46 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Issue with the hypothalamic segmentation

External Email - Use Caution Hi Andrew We are running Ubuntu 19.10 on our computer and as for Freesurfer were we tried to run this on freesurfer 7 and the development version but both produced this error. (freesurfer 7: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297 Freesurfer DEV: freesurfer-linux-centos8_x86_64-dev-20201109-2e16dca)

-Mackenzie

On Wed, Feb 3, 2021 at 10:37 AM Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> wrote: Hi Mackenzie,

Can you let us know what OS and version you’re running this on?

Thanks, Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Langan, Mackenzie <mackenzie.langan@icahn.mssm.edumailto:mackenzie.langan@icahn.mssm.edu> Date: Wednesday, February 3, 2021 at 10:31 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Issue with the hypothalamic segmentation

External Email - Use Caution Good Morning,

I have been trying to run the hypothalamic segmentation and get the following error:

aalqadi@athena:/zstore/data/aalqadi/aalqadi/mPFC/data$ mri_segment_hypothalamic_subunits --s S05486

Traceback (most recent call last):

File "/usr/local/freesurfer_dev/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 10, in <module>

import freesurfer as fs

File "/usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/__init__.py", line 8, in <module>

from . import bindings

ImportError: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not found (required by /usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/bindings.cpython-36m-x86_64-linux-gnu.sohttp://secure-web.cisco.com/1hzKok6ieorAQWILbwXrHm4nWv5aGVWrgLXUjICNL0HcYQDptT0fNHU6AOnJE3qXzhl9NRtNMMllRlwPcgtVISVPA9DsJir2pbwpc4pB0rKgOo_wc0yoGtFyiaXPXPRResPg1pGzrgr4u8Ao1pz7izacK37z0ZG3aoldmpUuq7kUqK3wyc40aHRkJp7A41zrUm-ikFytp9N0shHTbuPDQfnmsIvxVlN5ohXYytZXde24kCCukWp5zEZbAtWoVD6A8g0X2TtrYVzai92-jQmruSg/http%3A%2F%2Fbindings.cpython-36m-x86_64-linux-gnu.so%2F)

We installed the development version of freesurfer to see if that would work to run this, but that didn't work. We then installed XCRYPT_2.0 but still got the same error. We have two versions of python on our machine which we amended to fix the problem, but still get the same error. I am at a loss as to what I should try next to implement this. Any help would be great. Thanks

Best,

Mackenzie _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/19hlZ_7axUn8AdTxkDXxN0gm31q3caM72TmC2x6KVSreK-IU6x0CTaOcPOjHGpRK_JUcrqFsZGtksu7KzoHZ3M7IvU1I-PSoW3mwZfZPlkMfDr0w8PJi7iG-cJo6tQqplQqxsbReSDnnh2mp4SNSiqiGQqmGCDKIxLnGe30CHCQdxzwkM0ocR9hPP2z_PxjAv8na_c98JEJWleGzbUKkm1-DqCpOuLGoVxtk7hQ8HE9PMiSIybL2JDnJVlsg00XtK9BthcjsWGYHwS6Z-c4UQxA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer