[Bug]: Parsing AFNI script produces - Entity

[bclenet]

batch name and line

File : https://github.com/bids-standard/BEP028_BIDSprov/blob/master/examples/from_parsers/afni/afni_alt_onesided_proc.sub_001
Line 310

3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D

Note that I didn't check precisely but the same thing happens in other AFNI files.

What happened?

This line in the tcsh AFNI script

3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D

generates the following Entity in the json file

{
  "@id": "urn:4cef8fb6-2bfe-4c0e-85b8-4020e5ea01e3",
  "Label": "-",
  "AtLocation": "-",
  "GeneratedBy": "urn:1c42556b-6ea5-40c5-ba7f-d049ffbfac3c",
  "digest": {
    "sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
  }
},

Describe the expected ground-truth ?

The expected ground-truth :
We should create / reference these Entites instead:

• gmean.errts.unit.1D
• out.gcor.1D

What soft is concerned

AFNI

[bclenet]

This is caused by - according to the AFNI documentation on 3dTstat - the fact that the 3dTstat excutable has two signatures :

• One for processing 4D files, e.g. : 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc
• One for processing 1D files, e.g. : 3dTstat -stdev -bmv -prefix stdout: file.1D\' (the one described in this issue)