SPM12 handling of missing values in covariates

Summary of what happened:


I am working on a level 2 analysis using SPM in nipype and would like to include some neuropsychological data I have collected but I have missing data for certain subjects. I am also doing connectivity analyses in CONN with this data and CONN just requires that you insert “NaN” in your covariates wherever data is missing. I have tried to use the same covariate txt files in my spm nipype workflow and get an error stating

Unable to perform assignment because the left and right sides have a different number of elements.

which I don’t get when only including second level covariates with no missing values so I am assuming the error is related to how I am indicating that I have missing data.

How should I handle missing data in my second level covariates?

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


nipype 1.8.6 pypi_0

Running SPM version: 12.7771

FSLDIR: /apps/fsl/6.0.6/

FSL version: 6.0.6

Environment (Docker, Singularity, custom installation):

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

Relevant log outputs (up to 20 lines):

Screenshots / relevant information: