Here is the error (Error using spm_est_non_sphericity) I re-generated (i.e. everything default; Attempt 1). Model specification runs but estimation fails. It seemed like people get the same error commonly based on search. Below is the output from model specification.
Below is the error message.
Similar experiences others had:
I get the same error message when I change hrf setting to Inf (Attempt 2). Post 4, although not an error at the exactly same command line in the spm_est_non_sphericity or when doing the same analysis, gives some reasoning and solution of removing masking threshold (i.e. mthresh set at -Inf; Attempt 3). When I look at the fmriprep output, the values ranged like below. When smoothed with 6mm kernel the range changes. Although -Inf setting for masking threshold fixes the issue of ‘not running because of the spm_est_non_sphericity’ issue, this is when the larger implicit mask is generated. I assumed it may be because the smoothed data is used for input of this 1st level, and masking threshold is set at -Inf it is grabbing all the values that are numerically non-Zero.
(Attempt 5) Therefore I played around with different masking threshold values, such as 0.1, 0, -0.03. SPM spit out the same error message when the value was 0 or larger. Even if it ran without an error at negative values, the implicit mask is not correctly generated. Below is an example of -0.03 setting output, mask overlayed on smoothed data (input).
I could not find a reason how that could happen so I decided to use mask file generated from fmriprep as an explicit mask to set the boundary (Attempt 6), which ran without error, without making larger mask, and the above mentioned error happened in the next step.