Freesurfer License Error

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1

Hello,

I am trying to run a script using an Institution Server (Linux). Despite having my FreeSurfer License (for Linux) uploaded to the server, when I try to run the script, it fails and I receive this error:

Screen Shot 2022-06-24 at 9.25.47 AM
Screen Shot 2022-06-24 at 9.25.47 AM1360×114 68.2 KB

Every user on the team has their own license, and the script points to the current user’s license.

It is hard for my team and I to pinpoint this issue, because other members have not experienced it when they run the same script. Is there a reason why the script would fail for me and not others?

Thank you so much!

Kindly,
Sam

2

Hi,

I am guessing that the drive that contains your license wasn’t bound to your container when you ran fMRIPrep. What was your full command?

Best,
Steven

3

Hi Steven,

The single subject fmriprep script can be found here:

# === User input parameters ===
SUBJ=$1                                                                         # Read in from command line
THREADS=16
MEM=30
DUMMY_SCANS=2

BIDS_ROOT="/oak/stanford/groups/jzaki/scp_2022/bids"                            # Path to BIDS data
IMAGE=/"oak/stanford/groups/jzaki/zaki_images/fmriprep-20.2.1.simg"             # Path to singularity image
SURFER="/oak/stanford/groups/jzaki/zaki_images/FS_LICENSE.txt"                  # Path to FreeSurfer license
TFLOW="$HOME/.cache/templateflow"                                               # Path to templateflow sub-dir
mkdir -p $TFLOW                                                                 # Make templateflow dir if it doesn't exist


# === Run Singularity script ===
singularity run --home $HOME --cleanenv $IMAGE          \
  $BIDS_ROOT $BIDS_ROOT/derivatives                     \
  participant                                           \
  --participant-label $SUBJ                             \
  --task-id                                             \
      stressbuffer                                      \
  --md-only-boilerplate                                 \
  --fs-license-file $SURFER                             \
  --output-spaces                                       \
      MNI152NLin6Asym:res-2                             \
  --nthreads $THREADS                                   \
  --stop-on-first-crash                                 \
  --mem_mb $MEM                                         \
  --dummy-scans $DUMMY_SCANS

Are we missing an export somewhere? Thanks very much,
Ian

4

Yes, you should begin your singularity run with singularity run -B /oak and then include the rest of your call.

5

Good deal, thanks for your help!

1 Like
6

No problem, let me know if that fixes it for you!