🐛 Empty CSF mask with some subjects

[e-kenneally]

Describe the bug

Multiple users have reported this error when running the default pipeline, but only on some subjects. It happens regardless if CSF mask erosion is on or off.

ValueError: Number of time points in {subject}/nuisance_regressors_defaultNoGSR_140/_scan_scan_1/CerebrospinalFluid_mean/rest_calc_tshift_resample_volreg_calc_maths_flirt_roistat.1D (0) is inconsistent with length of functional file {subject}/_scan_scan_1/func_normalize_105/rest_calc_tshift_resample_volreg_calc_maths.nii.gz (433)

CSF mask for crashed subject:

CSF mask for normal subject:

To reproduce

No response

Preconfig

• [X] default
• [ ] abcd-options
• [ ] anat-only
• [ ] blank
• [ ] ccs-options
• [ ] fmriprep-options
• [ ] fx-options
• [ ] monkey
• [ ] monkey-ABCD
• [ ] ndmg
• [ ] nhp-macaque
• [ ] preproc
• [ ] rbc-options
• [ ] rodent

Custom pipeline configuration

No response

Run command

No response

Expected behavior

This might be a data-specific issue, in which case there should be a more informative error message. If not, these subjects should run to completion instead of crashing in nuisance regression, and the CSF masks should be populated.

Acceptance criteria

• [ ] More informative error message
• [ ] Fix / workaround for crash

Screenshots

No response

C-PAC version

No response

Container platform

No response

Docker and/or Singularity version(s)

No response

Additional context

No response

[e-kenneally]

It looks like in some cases this is caused by the lateral ventricles mask. I will open a PR to add a more descriptive error message when this happens.