Qsiprep missing dependencies error

Summary of what happened:

Hello everyone,I want to use qsipre to pre-process dwi images. But I got a problem as below. Does it have something to do with my freesurfer version?

Command used (and if a helper script was used, a link to the helper script or the command generated):

singularity run  -B /LabData2/qwl/BCP_for_test:/data:ro  \
 -B /LabData2/qwl/qsiprep_output:/out \
 -B /LabData2/qwl/qsi \
 -B prep_work:/work \
 -B /home/apps/freesurfer:/opt/freesurfer \
 --env FS_LICENSE=/opt/freesurfer/license.txt \
/LabData2/qwl/qsiprep/qsiprep.sif \
 /data /out participant \
--work-dir /work \
--output-resolution 1.5 \
--skip_bids_validation

Version:

Environment (Docker, Singularity / Apptainer, custom installation):

Singularity

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata.
  Falling back to 'CITATION'
Cannot run qsiprep. Missing dependencies:
        mri_synthstrip (Interface: FixHeaderSynthStrip)
        mri_synthstrip (Interface: FixHeaderSynthStrip)
        mri_synthstrip (Interface: FixHeaderSynthStrip)
        mri_synthstrip (Interface: FixHeaderSynthStrip)
        mri_synthstrip (Interface: FixHeaderSynthStrip)
        mri_synthseg (Interface: SynthSeg)

Screenshots / relevant information:


Hi @Shanbin_Zhang and welcome ot neurostars!

For future posts, please do not delete the prepopulated post template, which I added back in for you. It helps organize your post, prompts you for important information, and helps format the text for better readability.

Your problem comes from here:

That overrides the FreeSurfer version in the container. I would also, when you rerun, add the -e flag to the singularity run arguments (which tells Singularity to ignore your environment and instead use the FreeSurfer distribution within the container).

Best,
Steven

1 Like