[BUG] the default model includes n/a as another condition instead of ignoring it

[monique2208]

Is there an existing issue for this?

• I have searched the existing issues

Operating system

• Linux
• Mac
• Windows

Operating system version

No response

SPM 12 version

• 7771
• 7487
• 7219

Platform

• MATLAB
• Octave

Platform version

No response

bidspm version

v3.1.0

bidspm branch / commit number

No response

Expected Behavior

The default model should not add a model parameter for rows with n/a values.

BIDS stats model

{
  "Name": "default_onebacktask_model",
  "BIDSModelVersion": "1.0.0",
  "Description": "default BIDS stats model for onebacktask task",
  "Input": {
    "task": ["onebacktask"],
    "space": ["IXI549Space"]
  },
  "Nodes": [
    {
      "Level": "Run",
      "Name": "run",
      "GroupBy": [
        "run",
        "subject"
      ],
      "Transformations": {
        "Transformer": "",
        "Instructions": [
          {
            "Name": "",
            "Inputs": [""]
          }
        ]
      },
      "Model": {
        "X": [
          "trial_type.n/a",
          "trial_type.word",
          "1",
          "trans_?",
          "rot_?",
          "non_steady_state_outlier*",
          "motion_outlier*"
        ],
        "Type": "glm",
        "HRF": {
          "Variables": [
            "trial_type.n/a",
            "trial_type.word"
          ],
          "Model": "spm"
        },
        "Options": {
          "HighPassFilterCutoffHz": 0.008,
          "Mask": {
            "desc": ["brain"],
            "suffix": ["mask"]
          }
        },
        "Software": {
          "SPM": {
            "SerialCorrelation": "FAST",
            "InclusiveMaskingThreshold": 0.8
          }
        }
      },
      "Contrasts": [
        {
          "Name": "",
          "ConditionList": [""],
          "Weights": [""],
          "Test": "t"
        }
      ],
      "DummyContrasts": {
        "Test": "t",
        "Contrasts": [
          "trial_type.n/a",
          "trial_type.word"
        ]
      }
    },
    {
      "Level": "Subject",
      "Name": "subject",
      "GroupBy": [
        "subject",
        "contrast"
      ],
      "Model": {
        "X": [1],
        "Type": "glm"
      },
      "DummyContrasts": {
        "Test": "t"
      }
    },
    {
      "Level": "Dataset",
      "Name": "dataset",
      "GroupBy": [""],
      "Model": {
        "X": [1],
        "Type": "glm"
      },
      "DummyContrasts": {
        "Test": "t"
      }
    }
  ],
  "Edges": [
    {
      "Source": "run",
      "Destination": "subject"
    },
    {
      "Source": "subject",
      "Destination": "dataset"
    }
  ]
}

Current Behavior & Error message

The default model returns a model which also includes n/a as a value. As n/a is specified in a bids compliant way I think these rows should be ignored and not included in the model.

Anything else?

No response

[github-actions]

Thank you for your issue. Give us a little time to review it.

PS. You might want to check the FAQ if you haven't done so already.

This is an automated reply, generated by FAQtory

[Remi-Gau]

I suspect this is a bids matlab level issue. Will try to push a fix though my bandwidth is negative at the moment.

[monique2208]

Thank you for the quick response! It is easy to deal with in the meantime