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[BUG] GLM contrasting #1328

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4 of 9 tasks
CerenB opened this issue Nov 21, 2024 · 1 comment
Open
4 of 9 tasks

[BUG] GLM contrasting #1328

CerenB opened this issue Nov 21, 2024 · 1 comment
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bug 🐛 Something isn't working

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@CerenB
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CerenB commented Nov 21, 2024 •
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Is there an existing issue for this?

  • I have searched the existing issues

Operating system

  • Linux
  • Mac
  • Windows

Operating system version

  • Mac OS Version 10.15 "catalina"

SPM 12 version

  • 7771
  • 7487
  • 7219

Platform

  • MATLAB
  • Octave

Platform version

  • MATLAB 2017b

bidspm version

v3.1.0

bidspm branch / commit number

Expected Behavior

I'm certain that my issue is related to GLM model. I can run the GLM estimate but the contrast is giving an error.

Here is my script:

if GLM_FIRST_LEVEL
    
    for iSmooth = 1:length(fwhm)
        
        for i = 1:length(subject_label)
            
            % prepare to print the results
            results = defaultResultsStructure();
            
            opt.subjects = cell(1,1);
            
            results(1).nodeName = 'subject_level';
            results(1).name = {'Hand_gt_All','Feet_gt_All', ...
                               'Lips_gt_All', 'Tongue_gt_All', 'Forehead_gt_All'};
            
            results(1).MC = 'none';
            results(1).p = 0.001;
            results(1).k = 0;
            results(1).threshSpm = true();
            results(1).png = true();
            results(1).csv = true();
            results(1).binary = true();
            results(1).nidm = true();
            results(1).montage.do = true();
            results(1).montage.slices = 4:4:76;
            results(1).montage.orientation = 'axial';
            results(1).montage.background = struct('sub', opt.subjects{1}, ...
                                                   'suffix', 'T1w', ...
                                                   'desc', 'preproc', ...
                                                   'modality', 'anat');            
            results(2) = results;
            results(2).MC = 'FWE';
            results(2).p = 0.05;
            
            opt.results = results;
            
            bidspm(bids_dir, output_dir, 'subject', ...
                'action', 'stats', ...
                'participant_label', subject_label(i), ...
                'preproc_dir', preproc_dir, ...
                'model_file', model_file, ...
                'dry_run', dry_run, ...
                'verbosity', verbosity, ...
                'fwhm', fwhm{iSmooth}, ...
                'concatenate', false, ...
                'options', opt);
            
        end        
    end    
end

BIDS stats model

{
  "Name": "mototopy",
  "BIDSModelVersion": "1.0.0",
  "Description": "contrasts for the mototopy design dataset",
  "Input": {
    "task": [
      "mototopy"
    ],
    "space": [
      "T1w"
    ]
  },
  "Nodes": [
    {
      "Level": "Run",
      "Name": "run_level",
      "GroupBy": [
        "run",
        "subject"
      ],
      "Model": {
        "Type": "glm",
        "X": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead",
          "trial_type.hand_subjectCue",
          "trial_type.feet_subjectCue",
          "trial_type.tongue_subjectCue",
          "trial_type.lips_subjectCue",
          "trial_type.forehead_subjectCue",
          "trans_x", "trans_y", "trans_z", "rot_x", "rot_y", "rot_z"
        ],
        "HRF": {
          "Variables": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead"
          ],
          "Model": "spm"
        },
        "Options": {
          "HighPassFilterCutoffHz": 0.008,
          "Mask": {
            "suffix": [
              "mask"
            ],
            "desc": [
              "brain"
            ]
          }
        },
        "Software": {
          "SPM": {
            "InclusiveMaskingThreshold": "0.78",
            "SerialCorrelation": "FAST"
          }
        }
      },
      "DummyContrasts": {
        "Test": "t",
        "Contrasts": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead",
          "trial_type.hand_subjectCue",
          "trial_type.feet_subjectCue",
          "trial_type.tongue_subjectCue",
          "trial_type.lips_subjectCue",
          "trial_type.forehead_subjectCue"
        ]
      },
      "Contrasts": [
        {
          "Name": "Hand_gt_All",
          "ConditionList": [
            "trial_type.block_hand",
            "trial_type.block_feet",
            "trial_type.block_tongue",
            "trial_type.block_lips",
            "trial_type.block_forehead"
          ],
          "Weights": [1, -0.25, -0.25, -0.25, -0.25],
          "Test": "t"
        },
        {
         "Name": "Foot_gt_All",
          "ConditionList": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead"
          ],
          "Weights": [-0.25, 1, -0.25, -0.25, -0.25],
          "Test": "t"
        },
        {
         "Name": "Forehead_gt_All",
          "ConditionList": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead"
          ],
          "Weights": [-0.25, -0.25, -0.25, -0.25, 1],
          "Test": "t"
        },
        {
        "Name": "Lips_gt_All",
          "ConditionList": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead"
          ],
          "Weights": [-0.25, -0.25, -0.25, 1, -0.25],
          "Test": "t"
        },
        {
        "Name": "Tongue_gt_All",
          "ConditionList": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead"
          ],
          "Weights": [-0.25, -0.25, 1, -0.25, -0.25],
          "Test": "t"
        }
      ]
    },
    {
      "Level": "Subject",
      "Name": "subject_level",
      "GroupBy": [
        "contrast",
        "subject"
      ],
      "Model": {
        "Type": "glm",
        "X": [
          1
        ]
      },
      "DummyContrasts": {
        "Test": "t"
      }
    },
    {
      "Level": "Dataset",
      "Name": "dataset_level",
      "GroupBy": [
        "contrast"
      ],
      "Model": {
        "X": [
          1
        ],
        "Type": "glm",
        "Software": {
          "SPM": {
            "SerialCorrelation": "FAST"
          }
        }
      },
      "DummyContrasts": {
        "Test": "t"
      }
    }
  ]
}

Current Behavior & Error message

K>> contrasts(weightVectorIsAllZero).name
Function 'subsindex' is not defined for values
of class 'cell'.
 
K>> weightVectorIsAllZero

weightVectorIsAllZero =

  1×66 cell array

  Columns 1 through 5

    {[0]}    {[0]}    {[0]}    {[0]}    {[0]}

  Columns 6 through 10

    {[0]}    {[0]}    {[0]}    {[0]}    {[0]}

  Columns 11 through 15

    {[0]}    {[0]}    {[0]}    {[0]}    {[0]}

  Columns 16 through 20

    {[0]}    {[0]}    {[0]}    {[0]}    {[0]}

  Columns 21 through 25

    {[0]}    {[0]}    {[0]}    {[0]}    {[0]}

  Columns 26 through 30

    {[0]}    {[0]}    {[0]}    {[0]}    {[0]}

  Columns 31 through 35

    {[0]}    {[0]}    {[0]}    {[0]}    {[0]}

  Columns 36 through 40

    {[0]}    {[0]}    {[0]}    {[0]}    {[0]}

  Columns 41 through 45

    {[0]}    {[0]}    {[0]}    {[0]}    {[0]}

  Columns 46 through 50

    {[0]}    {[0]}    {[0]}    {[0]}    {[0]}

  Columns 51 through 55

    {[0]}    {[0]}    {[0]}    {[0]}    {[0]}

  Columns 56 through 60

    {[0]}    {[0]}    {[0]}    {[0]}    {[0]}

  Columns 61 through 65

    {[0]}    {[0]}    {[0]}    {[0]}    {[0]}

  Column 66

    {[1]}


[14:50:26] bidspm - INFO				
Function 'subsindex' is not defined for values of class 'cell'.
 Error MATLAB:UndefinedFunction occurred:
	- Error in validateContrasts
		line 30 in /Volumes/extreme/Cerens_files/fMRI/moebius_topo_analyses/code/src/bidspm-stats/../../lib/bidspm/src/stats/utils/validateContrasts.m
	- Error in appendContrast
		line 32 in /Volumes/extreme/Cerens_files/fMRI/moebius_topo_analyses/code/src/bidspm-stats/../../lib/bidspm/src/stats/subject_level/appendContrast.m
	- Error in addExplicitDummyContrasts
		line 138 in /Volumes/extreme/Cerens_files/fMRI/moebius_topo_analyses/code/src/bidspm-stats/../../lib/bidspm/src/stats/subject_level/specifyDummyContrasts.m
	- Error in specifyDummyContrasts
		line 37 in /Volumes/extreme/Cerens_files/fMRI/moebius_topo_analyses/code/src/bidspm-stats/../../lib/bidspm/src/stats/subject_level/specifyDummyContrasts.m
	- Error in specifyContrasts
		line 64 in /Volumes/extreme/Cerens_files/fMRI/moebius_topo_analyses/code/src/bidspm-stats/../../lib/bidspm/src/stats/subject_level/specifyContrasts.m
	- Error in setBatchSubjectLevelContrasts
		line 42 in /Volumes/extreme/Cerens_files/fMRI/moebius_topo_analyses/code/src/bidspm-stats/../../lib/bidspm/src/batches/stats/setBatchSubjectLevelContrasts.m
	- Error in bidsFFX
		line 120 in /Volumes/extreme/Cerens_files/fMRI/moebius_topo_analyses/code/src/bidspm-stats/../../lib/bidspm/src/workflows/stats/bidsFFX.m
	- Error in runContrasts
		line 127 in /Volumes/extreme/Cerens_files/fMRI/moebius_topo_analyses/code/src/bidspm-stats/../../lib/bidspm/src/cli/cliStats.m
	- Error in cliStats
		line 86 in /Volumes/extreme/Cerens_files/fMRI/moebius_topo_analyses/code/src/bidspm-stats/../../lib/bidspm/src/cli/cliStats.m
	- Error in executeAction
		line 86 in /Volumes/extreme/Cerens_files/fMRI/moebius_topo_analyses/code/src/bidspm-stats/../../lib/bidspm/bidspm.m
	- Error in bidspm
		line 26 in /Volumes/extreme/Cerens_files/fMRI/moebius_topo_analyses/code/src/bidspm-stats/../../lib/bidspm/bidspm.m

ERROR LOG SAVED:
	/Volumes/extreme/Cerens_files/fMRI/moebius_topo_analyses/outputs/derivatives/error_logs/error_2024-11-21T14-50.log
Use it when opening an issue:
	https://github.com/cpp-lln-lab/bidspm/issues/new/choose.

Function 'subsindex' is not defined for values of class
'cell'.

Error in validateContrasts (line 30)
    names = contrasts(weightVectorIsAllZero).name;

Error in appendContrast (line 32)
  validateContrasts(contrasts);

Error in
specifyDummyContrasts>addExplicitDummyContrasts (line
138)
        [contrasts, counter] =
        appendContrast(contrasts, C, counter,
        testType);

Error in specifyDummyContrasts (line 37)
  [contrasts, counter] =
  addExplicitDummyContrasts(model, node, contrasts,
  counter);

Error in specifyContrasts (line 64)
    [contrasts, counter] = specifyDummyContrasts(model,
    node, contrasts, counter);

Error in setBatchSubjectLevelContrasts (line 42)
    contrasts = specifyContrasts(bm, SPM);

Error in bidsFFX (line 120)
        matlabbatch =
        setBatchSubjectLevelContrasts(matlabbatch, opt,
        subLabel, nodeName);

Error in cliStats>runContrasts (line 127)
    bidsFFX('contrasts', opt);

Error in cliStats (line 86)
        runContrasts(isSubjectLevel, opt, nodeName,
        concatenate);

Error in bidspm>executeAction (line 86)
      cliStats(varargin{2:end});

Error in bidspm (line 26)
    returnCode = executeAction(action, varargin{:});

error_2024-11-21T14-50.log

Anything else?

No response
@CerenB CerenB added the bug 🐛 Something isn't working label Nov 21, 2024
@CerenB CerenB changed the title [BUG] [BUG] GLM contrasting Nov 22, 2024
@CerenB
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CerenB commented Nov 22, 2024

I did change the model file, but still have the same error.

Function 'subsindex' is not defined for values of class 'cell'.

{
  "Name": "mototopy",
  "BIDSModelVersion": "1.0.0",
  "Description": "contrasts for the mototopy design dataset",
  "Input": {
    "task": [
      "mototopy"
    ],
    "space": [
      "T1w"
    ]
  },
  "Nodes": [
    {
      "Level": "Run",
      "Name": "run_level",
      "GroupBy": [
        "run",
        "subject"
      ],
      "Model": {
        "Type": "glm",
        "X": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead",
          "trial_type.hand_subjectCue",
          "trial_type.feet_subjectCue",
          "trial_type.tongue_subjectCue",
          "trial_type.lips_subjectCue",
          "trial_type.forehead_subjectCue",
          "trans_x", "trans_y", "trans_z", "rot_x", "rot_y", "rot_z"
        ],
        "HRF": {
          "Variables": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead"
          ],
          "Model": "spm"
        },
        "Options": {
          "HighPassFilterCutoffHz": 0.008,
          "Mask": {
            "suffix": [
              "mask"
            ],
            "desc": [
              "brain"
            ]
          }
        },
        "Software": {
          "SPM": {
            "InclusiveMaskingThreshold": "0.78",
            "SerialCorrelation": "FAST"
          }
        }
      },
      "DummyContrasts": {
        "Test": "t",
        "Contrasts": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead",
          "trial_type.hand_subjectCue",
          "trial_type.feet_subjectCue",
          "trial_type.tongue_subjectCue",
          "trial_type.lips_subjectCue",
          "trial_type.forehead_subjectCue"
        ]
      }
    },
    {
      "Level": "Subject",
      "Name": "subject_level",
      "GroupBy": [
        "contrast",
        "subject"
      ],
      "Model": {
        "Type": "glm",
        "X": [
          1
        ]
      },
      "Contrasts": [
        {
          "Name": "Hand_gt_All",
          "ConditionList": [
            "trial_type.block_hand",
            "trial_type.block_feet",
            "trial_type.block_tongue",
            "trial_type.block_lips",
            "trial_type.block_forehead"
          ],
          "Weights": [1, -0.25, -0.25, -0.25, -0.25],
          "Test": "t"
        },
        {
         "Name": "Foot_gt_All",
          "ConditionList": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead"
          ],
          "Weights": [-0.25, 1, -0.25, -0.25, -0.25],
          "Test": "t"
        },
        {
         "Name": "Forehead_gt_All",
          "ConditionList": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead"
          ],
          "Weights": [-0.25, -0.25, -0.25, -0.25, 1],
          "Test": "t"
        },
        {
        "Name": "Lips_gt_All",
          "ConditionList": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead"
          ],
          "Weights": [-0.25, -0.25, -0.25, 1, -0.25],
          "Test": "t"
        },
        {
        "Name": "Tongue_gt_All",
          "ConditionList": [
          "trial_type.block_hand",
          "trial_type.block_feet",
          "trial_type.block_tongue",
          "trial_type.block_lips",
          "trial_type.block_forehead"
          ],
          "Weights": [-0.25, -0.25, 1, -0.25, -0.25],
          "Test": "t"
        }
      ],
      "DummyContrasts": {
        "Test": "t"
      }
    },
    {
      "Level": "Dataset",
      "Name": "dataset_level",
      "GroupBy": [
        "contrast"
      ],
      "Model": {
        "X": [
          1
        ],
        "Type": "glm",
        "Software": {
          "SPM": {
            "SerialCorrelation": "FAST"
          }
        }
      },
      "DummyContrasts": {
        "Test": "t"
      }
    }
  ]
}

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