TraitError: The 'tis' trait of a _BASILCBFInputSpec instance must be a float or a list of items which are a float

[LuRoe7]

I am trying to run ASLprep 0.2.8 as a singularity container via Slurm. I use the following command:

singularity run --cleanenv
-B /data/core-psy/data/lroell/hcpold:/data
-B /data/core-psy/data/lroell/output_asl:/out
-B /data/core-psy/data/lroell/wd_asl:/workdir
-B /data/core-psy/data/lroell/tmp_asl:/home/aslprep
--home /home/aslprep
/data/core-psy/data/lroell/aslprep-0.2.8.simg /data/ /out participant
--participant_label HCPOLD0001
--skip-bids-validation
--output-spaces MNI152NLin2009cAsym:res-2
--asl2t1w-init register
--asl2t1w-dof 12
--force-bbr
--scorescrub
--basil
--skull-strip-t1w force
--dummy-vols 10
--verbose
--n_cpus 16
--mem 32000
-w /workdir/ \

After a few seconds it throws an error:

traits.trait_errors.TraitError: The 'tis' trait of a _BASILCBFInputSpec instance must be a float or a list of items which are a float, but a value of array([1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 1.7, 2.2,2.2, 2.2, 2.2, 2.2, 2.2, 2.2, 2.2, 2.2, 2.2, 2.2, 2.2, 2.7, 2.7,
2.7, 2.7, 2.7, 2.7, 2.7, 2.7, 2.7, 2.7, 2.7, 2.7, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2, 3.2,
3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7, 3.7,
1.5, 1.5, 1.5, 1.5]) <class 'numpy.ndarray'> was specified.

This array corresponds to the sum of every element of the PostLabelingDelay array and the LabelingDuration of 1.5 sec I specified in the .json files:

"PostLabelingDelay": [0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.7,0.7,0.7,0.7,0.7,0.7,0.7,0.7,0.7,0.7,0.7,0.7,1.2,1.2,1.2,1.2,1.2,1.2,1.2,1.2,1.2,1.2,1.2,1.2,1.7,1.7,1.7,1.7,1.7,1.7,1.7,1.7,1.7,1.7,1.7,1.7,1.7,1.7,1.7,1.7,1.7,1.7,1.7,1.7,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.22.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,2.2,0.0,0.0,0.0,0.0]
"LabelingDuration": 1.5

It seems like the tis trait of the _BASILCBFInputSpec instance requires a list as input and cannot handle numpy arrays. How do I have to specify the PostLabelingDelay in order to make it a list?

[philjohnston]

I'm also experiencing the same error when trying to run ASLprep 0.2.8 via Singularity on PASL data, but I only have a single 'PostLabelingDelay' value.

The command:
singularity run --cleanenv -B /project/def-rmcintos/pjohns/stroke_BIDS:/base aslprep-latest.simg
--participant-label 10450 --skip_bids_validation --scorescrub --fs-license-file $HOME/license/license.txt
-vvv
/base/NIFTI/
/base/derivatives/
participant

The error:
traits.trait_errors.TraitError: The 'tis' trait of a _BASILCBFInputSpec instance must be a float or a list of items which are a float, but a value of array(1.1) <class 'numpy.ndarray'> was specified.

[philjohnston]

Thank you for the very quick turnaround on this. Forgive my ignorance about singularity, but will this change take effect if I simply reinstall the singularity image? If not, is there anything else I can do in the meantime? Thanks

[tsalo]

It looks like there was an issue deploying to DockerHub, so I just fixed that. You can access the recent changes by pulling the pennlinc/aslprep:unstable Docker image.

[philjohnston]

Thank you. I tried the same call as above with the aslprep:unstable image, and now receive the following:

230301-15:15:21,481 nipype.workflow IMPORTANT:
         ASLPrep started!
230301-15:15:21,854 nipype.workflow CRITICAL:
         ASLPrep failed: module 'networkx' has no attribute 'to_scipy_sparse_matrix'

This seems to be related to this change to Networkx with version 3.0: https://networkx.org/documentation/latest/release/migration_guide_from_2.x_to_3.0.html#replacing-numpy-scipy-matrices-with-arrays

[tsalo]

Thanks. I've opened a new issue about this and will push a fix ASAP.

[tsalo]

@philjohnston you should be able to pull the new version of unstable now.