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