External Email - Use Caution
Hi all,
I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity image (pulled from the FreeSurfer DockerHub) like this:
export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt export SINGULARITYENV_SUBJECTS_DIR=/mnt/22Q/data/freesurfer
singularity exec --cleanenv -B /project/bbl_projects/22Q/:/mnt/22Q \ /project/bbl_projects/22Q/images/freesurfer_7.1.1.sif \ recon-all -s sub-17867 -i /mnt/22Q/data/bids_directory/sub-17867/ses-22Q1/anat/sub-17867_ses-22Q1_T1w.nii.gz -all
But it fails quickly with error message:
ERROR: crypt() returned null with 4-line file
Do you know what might be causing this error message? How can I address this?
Additional info:
1. FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 2. uname -a: Linux singularity01 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 3. recon-all.log: see attached
See GitHub issue: https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDp...
[https://secure-web.cisco.com/1TDcdfVeSPTzDeg0asgP7Yy7WKhWmvgHB9T_fyDNBmSSR44...https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848 `ERROR: crypt() returned null with 4-line file` when running via Singularity image · Issue #848 · freesurfer/freesurferhttps://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848 I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity image like this: export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt export SINGULARITYENV_SUBJECTS_DIR=/mnt/22... github.com
Thank you for any assistance!
Katja Zoner
Hi Katja,
I wonder if this is related to possible security settings. I can’t replicate this, but can you send your license file so that we can narrow down the possibilities? You can send it directly to my email, off-list.
Best Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zoner, Katja Katja.Zoner@pennmedicine.upenn.edu Date: Monday, March 22, 2021 at 2:40 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] "ERROR: crypt() returned null with 4-line file" when running via Singularity
External Email - Use Caution Hi all,
I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity image (pulled from the FreeSurfer DockerHub) like this:
export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt
export SINGULARITYENV_SUBJECTS_DIR=/mnt/22Q/data/freesurfer
singularity exec --cleanenv -B /project/bbl_projects/22Q/:/mnt/22Q \
/project/bbl_projects/22Q/images/freesurfer_7.1.1.sif \
recon-all -s sub-17867 -i /mnt/22Q/data/bids_directory/sub-17867/ses-22Q1/anat/sub-17867_ses-22Q1_T1w.nii.gz -all
But it fails quickly with error message:
ERROR: crypt() returned null with 4-line file
Do you know what might be causing this error message? How can I address this?
Additional info:
1. FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 2. uname -a: Linux singularity01 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 3. recon-all.log: see attached
See GitHub issue: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/freesurfer/freesurfer/issues/848https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848 [https://secure-web.cisco.com/1TDcdfVeSPTzDeg0asgP7Yy7WKhWmvgHB9T_fyDNBmSSR44...]https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848 `ERROR: crypt() returned null with 4-line file` when running via Singularity image · Issue #848 · freesurfer/freesurferhttps://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848 I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity image like this: export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt export SINGULARITYENV_SUBJECTS_DIR=/mnt/22... github.com
Thank you for any assistance!
Katja Zoner
External Email - Use Caution
Hi Andrew,
After speaking with our compute cluster service providers, it seems like this error is due to FIPS being enabled on the cluster. Are there any existing solutions to FIPS conflicts with FreeSurfer?
Thanks! Katja ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Saturday, March 27, 2021 4:19 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] "ERROR: crypt() returned null with 4-line file" when running via Singularity
Hi Katja,
I wonder if this is related to possible security settings. I can’t replicate this, but can you send your license file so that we can narrow down the possibilities? You can send it directly to my email, off-list.
Best
Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zoner, Katja Katja.Zoner@pennmedicine.upenn.edu Date: Monday, March 22, 2021 at 2:40 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] "ERROR: crypt() returned null with 4-line file" when running via Singularity
External Email - Use Caution
Hi all,
I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity image (pulled from the FreeSurfer DockerHub) like this:
export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt
export SINGULARITYENV_SUBJECTS_DIR=/mnt/22Q/data/freesurfer
singularity exec --cleanenv -B /project/bbl_projects/22Q/:/mnt/22Q \
/project/bbl_projects/22Q/images/freesurfer_7.1.1.sif \
recon-all -s sub-17867 -i /mnt/22Q/data/bids_directory/sub-17867/ses-22Q1/anat/sub-17867_ses-22Q1_T1w.nii.gz -all
But it fails quickly with error message:
ERROR: crypt() returned null with 4-line file
Do you know what might be causing this error message? How can I address this?
Additional info:
1. FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 2. uname -a: Linux singularity01 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 3. recon-all.log: see attached
See GitHub issue: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZP-G-Xr8XEEs0FjfX-BNQ2MTzIYHR23dYM7sFuOgG6iSe1...https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848
[https://secure-web.cisco.com/1TDcdfVeSPTzDeg0asgP7Yy7WKhWmvgHB9T_fyDNBmSSR44...]https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848
`ERROR: crypt() returned null with 4-line file` when running via Singularity image · Issue #848 · freesurfer/freesurferhttps://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848
I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity image like this: export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt export SINGULARITYENV_SUBJECTS_DIR=/mnt/22...
github.com
Thank you for any assistance!
Katja Zoner
Hi Katja,
Okay good to know. I will follow up off-list.
Best, Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zoner, Katja Katja.Zoner@pennmedicine.upenn.edu Date: Tuesday, March 30, 2021 at 1:24 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: "ERROR: crypt() returned null with 4-line file" when running via Singularity
External Email - Use Caution Hi Andrew,
After speaking with our compute cluster service providers, it seems like this error is due to FIPS being enabled on the cluster. Are there any existing solutions to FIPS conflicts with FreeSurfer?
Thanks! Katja ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Saturday, March 27, 2021 4:19 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] "ERROR: crypt() returned null with 4-line file" when running via Singularity
Hi Katja,
I wonder if this is related to possible security settings. I can’t replicate this, but can you send your license file so that we can narrow down the possibilities? You can send it directly to my email, off-list.
Best
Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zoner, Katja Katja.Zoner@pennmedicine.upenn.edu Date: Monday, March 22, 2021 at 2:40 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] "ERROR: crypt() returned null with 4-line file" when running via Singularity
External Email - Use Caution
Hi all,
I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity image (pulled from the FreeSurfer DockerHub) like this:
export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt
export SINGULARITYENV_SUBJECTS_DIR=/mnt/22Q/data/freesurfer
singularity exec --cleanenv -B /project/bbl_projects/22Q/:/mnt/22Q \
/project/bbl_projects/22Q/images/freesurfer_7.1.1.sif \
recon-all -s sub-17867 -i /mnt/22Q/data/bids_directory/sub-17867/ses-22Q1/anat/sub-17867_ses-22Q1_T1w.nii.gz -all
But it fails quickly with error message:
ERROR: crypt() returned null with 4-line file
Do you know what might be causing this error message? How can I address this?
Additional info:
1. FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 2. uname -a: Linux singularity01 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 3. recon-all.log: see attached
See GitHub issue: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/freesurfer/freesurfer/issues/848https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848
[https://secure-web.cisco.com/1TDcdfVeSPTzDeg0asgP7Yy7WKhWmvgHB9T_fyDNBmSSR44...]https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848
`ERROR: crypt() returned null with 4-line file` when running via Singularity image · Issue #848 · freesurfer/freesurferhttps://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848
I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity image like this: export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt export SINGULARITYENV_SUBJECTS_DIR=/mnt/22...
github.com
Thank you for any assistance!
Katja Zoner
freesurfer@nmr.mgh.harvard.edu
-
Hoopes, Andrew -
Zoner, Katja