Dependency Error in QSIPrep

1

Hi,

I am trying to run qsiprep using field map input. We have specified the fieldmap in the “IntendedFor” fields in the JSON side cars. We are also processing using fmriprep pipeline and that works with the same fmaps.

However, qsiprep does not run. I am getting the following error:
[WARNING] This document format requires a nonempty element.
Please specify either ‘title’ or ‘pagetitle’ in the metadata.
Falling back to ‘CITATION’
Cannot run qsiprep. Missing dependencies:
fugue (Interface: FUGUE)
fugue (Interface: FUGUE)
prelude (Interface: PRELUDE)

Does this have to do with eddy-config option?

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2

This is my command: singularity run --cleanenv -B /mnt/cina/WMH:/WMH /mnt/cina/WMH/lib/qsiprep-0.15.2.sif /WMH/data/BIDS/ADNI/ /WMH/data/BIDS/ADNI/derivatives/qsiprep participant --participant_label sub-002S0413 --output-resolution 1.0 --fs_license_file /WMH/lib/fs_license.txt --freesurfer_input /WMH/data/BIDS/ADNI/derivatives/qsiprep/qsiprep/sourcedata/freesurfer --skip-bids-validation

3

Hi,

Please update to 0.16.1 which is on dockerhub. It should have those dependencies installed in the container.

Best,
Steven

4

I ran qsiprep on 0.16.1 but encountered some errors. Half of the brain was missing when I viewed the preproc file on fsleyes.

5

Hi,

This sounds like a different issue that should be on a new thread, or perhaps posted on the QSIPrep github repo issues page.

Best,
Steven