`bidsSpatialPrepro(opt)` does not run without prior slice time correction

[marcobarilari]

Describe your problem in detail

in the latest dev branch, bidsSpatialPrepro(opt) does not work if STC has not been run.

Describe what outcome you expected

To run spatial prepro without STC as first step, this is possible in previous releases right?

Describe what you got instead

Error message

If possible paste below the error message you encountered.

WORKFLOW: SPATIAL PREPROCESSING

 PROCESSING SUBJECT No.: 1 SUBJECT ID : pilot001 

 BUILDING JOB: selecting anatomical image

 BUILDING JOB: realign
Error using validationInputFile (line 62)
This file does not exist:
/Users/barilari/Desktop/data_temp/ses-006_cpp_spm/derivatives/cpp_spm-task-mtMstLocalizerWithStatic/sub-pilot001/ses-006/func/asub-pilot001_ses-006_task-mtMstLocalizerWithStatic_run-001_bold.nii[.gz]

Error in setBatchRealign (line 91)
      file = validationInputFile(subFuncDataDir, boldFilename, prefix);

Error in bidsSpatialPrepro (line 50)
  parfor iSub = 1:numel(opt.subjects)

[Remi-Gau]

To run spatial prepro without STC as first step, this is possible in previous releases right?

Nope. Pretty sure that STC would always be run if sufficient info is provided (slice timing info in the json file of BIDS, or inputed in the options structure).

But we could add a opt.stc.skip flag if there is a need.

[marcobarilari]

you are right, at least in v1.0.0 I can't run bidsSpatialPrepro(opt); without an a*.nii file.

Do you think it could be useful? The direction here is to deprecate preprocesing from SPM in favor of fMRIprep so might be a waste of time.