Address possible v1.8.5 issue(s) regarding surface post-proc

[e-kenneally]

1. ABCD-options: The following files created in postfreesurfer are corrupt in multiple runs (doesn't happen for every subject): L/R.sphere.reg.surf.gii L/R.sphere.LR.reg.surf.gii
2. fmriprep-options: the input (repetition_time) in function tr_string_to_float is NoneType

[shnizzedy]

For 2, I believe that only happens if RepetitionTime is missing from the sidecar or if the sidecar is missing.

[e-kenneally]

Update: specifying RepetitionTime in the data config 'scan' is a patch fix for this error.

func-1:
      scan: /path/to/image
      scan_parameters: {
            RepetitionTime: 0.8
      }

Also, re Jon's comment, the JSON file had repetition time but it still threw the error.

[e-kenneally]

Update again on fmriprep error: the func json file was missing from scan_parameters in Nathalia's data config file. I'm going to write a check to make sure it can't get that far without it, but that's why the error never surfaced in regression testing.

[sgiavasis]

Update:

While running: wb_command

-surface-apply-warpfield /ocean/projects/med220004p/agutierr/abcd_log_subprocess/abcd-options/HNU_1/working/pipeline_abcd-options-seed/cpac_sub-0025428_ses-1/post_freesurfer_246/T1w/Native/sub-0025428_ses-1.L.white.native.surf.gii /ocean/projects/med220004p/agutierr/abcd_log_subprocess/abcd-options/HNU_1/working/pipeline_abcd-options-seed/cpac_sub-0025428_ses-1/post_freesurfer_246/MNINonLinear/xfms/standard2acpc_dc.nii.gz /ocean/projects/med220004p/agutierr/abcd_log_subprocess/abcd-options/HNU_1/working/pipeline_abcd-options-seed/cpac_sub-0025428_ses-1/post_freesurfer_246/MNINonLinear/Native/sub-0025428_ses-1.L.white.native.surf.gii

-fnirt /ocean/projects/med220004p/agutierr/abcd_log_subprocess/abcd-options/HNU_1/working/pipeline_abcd-options-seed/cpac_sub-0025428_ses-1/post_freesurfer_246/MNINonLinear/xfms/acpc_dc2standard.nii.gz

ERROR: surface exceeds the bounding box of the warpfield

• Need to isolate this error in the post-Freesurfer script and see why only this specific data is triggering this error.
• Possibly, this error was introduced after recent additions to develop, possibly related to ACPC alignment connections.

[sgiavasis]

See the linked PR #1932 for the continuation. @amygutierrez will ascertain if the change in desc-preproc_T1w is explained due to changes in develop for abcd-options, notably the ordering fix from @e-kenneally regarding ACPC alignment and brain extraction.