Qsiprep + atlas_2_ref + invert_transform_flags

Dear all,
I have been running qsiprep singularity container. I keep having the following issues independently of my inputs. Any help would be much appreciated:
“Node atlas_2_ref failed to run on host XX”
" “ERROR: The invert_transform_flags list must have the same number "
ValueError: ERROR: The invert_transform_flags list must have the same number of entries as the transforms list.”
Such issue was not often reported. I do have in my script " --template MNI152NLin2009cAsym"
Anything else i can try?

That argument, --template MNI152NLin2009cAsym is deprecated, try taking it out. QSIPrep diffusion derivatives are only in subject space (there are some anatomical outputs in MNI).

thanks for the reply. I also tried removing it with the same outcome.

What version of QSIPrep are you using, and what does your command look like? Maybe try using a new cache dir after removing the template argument?

-QSIprep image: qsiprep-0.12.2.sif
singularity run --cleanenv -B ${bids_root_dir} $image
$bids_root_dir/rawdata bids_root_dir/derivatives \ participant \ --participant-label {sub}
–fs-license-file $bids_root_dir/derivatives/license.txt
–dwi-denoise-window 5
–output-resolution 1
–hmc-model eddy
–recon_spec mrtrix_multishell_msmt

  • could you please be more explicit with how to use " a new cache dir "?
    thank you
  1. Try updating to the most recent stable release (0.14.3)
  2. Specify a new $WORK_DIR in the -w argument

Also, --dwi-only will not work with the --recon_spec you’ve specified. You will need to run through the anatomical workflow to do reconstruction.

Thanks Steven,
QSIPrep running smoothly now…