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[BUG] Group level stops at 'MA: inspect goodness of fit' #1237

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4 of 9 tasks
marcobarilari opened this issue May 3, 2024 · 4 comments
Open
4 of 9 tasks

[BUG] Group level stops at 'MA: inspect goodness of fit' #1237

marcobarilari opened this issue May 3, 2024 · 4 comments
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bug 🐛 Something isn't working

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@marcobarilari
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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

  • Linux Ubuntu 22.04 "jammy jellyfish"

SPM 12 version

  • 7771
  • 7487
  • 7219

Platform

  • MATLAB
  • Octave

Platform version

  • MATLAB 2018a

bidspm version

v3.1.0

bidspm branch / commit number

branch =

'main'

commit =

'cdca7dd4'

Expected Behavior

To run group level, no idea how to debug it

BIDS stats model

{
  "Name": "visualMotLoc",
  "BIDSModelVersion": "1.0.0",
  "Description": "contrasts for the visual motion localizer",
  "Input": {
    "task": [
      "visualLocalizer"
    ],
    "space": [
      "IXI549Space"
    ]
  },
  "Nodes": [
    {
      "Level": "Run",
      "Name": "run_level",
      "GroupBy": [
        "run",
        "subject"
      ],
      "Model": {
        "Type": "glm",
        "X": [
          "trial_type.static",
          "trial_type.motion",
          "trial_type.response",
          "trans_?",
          "rot_?"
        ],
        "HRF": {
          "Variables": [
            "trial_type.static",
            "trial_type.motion",
            "trial_type.response"
          ],
          "Model": "spm+derivative"
        },
        "Options": {
          "HighPassFilterCutoffHz": 0.008
        },
        "Software": {
          "SPM": {
            "InclusiveMaskingThreshold": 0.8,
            "SerialCorrelation": "FAST"
          }
        }
      },
      "DummyContrasts": {
        "Test": "t",
        "Contrasts": [
          "trial_type.static",
          "trial_type.motion",
          "trial_type.response"
        ]
      },
      "Contrasts": [
        {
          "Name": "static_gt_motion",
          "ConditionList": [
            "trial_type.static",
            "trial_type.motion"
          ],
          "Weights": [
            1,
            -1
          ],
          "Test": "t"
        },
        {
          "Name": "motion_gt_static",
          "ConditionList": [
            "trial_type.static",
            "trial_type.motion"
          ],
          "Weights": [
            -1,
            1
          ],
          "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": {
        "Type": "glm",
        "X": [
          1
        ]
      },
      "DummyContrasts": {
        "Test": "t"
      }
    }
  ]
}

Current Behavior & Error message

[11:18:53] bidspm - INFO				
bidspm already initialized

[11:18:53] bidspm - INFO				
Validating bids dataset:
 /mnt/HD_jupiter/marcobarilari/datalad/analysis_high-res_BLAM_biMotion_localizers/code/src/../../inputs/raw

[11:18:53] bidspm - INFO				
bidspm already initialized
Warning:
Could not find a corresponding Node with
  Name: "dataset"; Level: ""

  Available nodes:
	- Name: "run_level"; Level: "Run"
	- Name: "subject_level"; Level: "Subject"
	- Name: "dataset_level"; Level: "Dataset"

 
> In bids.internal.error_handling (line 60)
  In bids.Model/get_nodes (line 354)
  In getDummyContrastsList (line 24)
  In boilerplate (line 137)
  In cliStats (line 58)
  In bidspm>executeAction (line 86)
  In bidspm (line 26)
  In runAnalyses_visualLocalizer_MNI_groupStats (line 48) 
Warning: Could not find key 'designType' 
> In get_key (line 74)
  In renderer (line 159)
  In octache (line 79)
  In boilerplate (line 185)
  In cliStats (line 58)
  In bidspm>executeAction (line 86)
  In bidspm (line 26)
  In runAnalyses_visualLocalizer_MNI_groupStats (line 48) 


------------------------------------------------------------------------
03-May-2024 11:19:21 - Running job #6
------------------------------------------------------------------------
03-May-2024 11:19:21 - Running 'Smooth'
03-May-2024 11:19:24 - Done    'Smooth'
03-May-2024 11:19:24 - Running 'Smooth'
03-May-2024 11:19:27 - Done    'Smooth'
03-May-2024 11:19:27 - Running 'Smooth'
03-May-2024 11:19:31 - Done    'Smooth'
03-May-2024 11:19:31 - Running 'Smooth'
03-May-2024 11:19:34 - Done    'Smooth'
03-May-2024 11:19:34 - Running 'Smooth'
03-May-2024 11:19:36 - Done    'Smooth'
03-May-2024 11:19:36 - Running 'Smooth'
03-May-2024 11:19:40 - Done    'Smooth'
03-May-2024 11:19:40 - Running 'Smooth'
03-May-2024 11:19:44 - Done    'Smooth'
03-May-2024 11:19:44 - Running 'Smooth'
03-May-2024 11:19:46 - Done    'Smooth'
03-May-2024 11:19:46 - Running 'Smooth'
03-May-2024 11:19:50 - Done    'Smooth'
03-May-2024 11:19:50 - Running 'Smooth'
03-May-2024 11:19:52 - Done    'Smooth'
03-May-2024 11:19:52 - Running 'Smooth'
03-May-2024 11:19:55 - Done    'Smooth'
03-May-2024 11:19:55 - Running 'Smooth'
03-May-2024 11:19:57 - Done    'Smooth'
03-May-2024 11:19:57 - Running 'Smooth'
03-May-2024 11:20:00 - Done    'Smooth'
03-May-2024 11:20:00 - Done



------------------------------------------------------------------------
03-May-2024 11:21:23 - Running job #6
------------------------------------------------------------------------
03-May-2024 11:21:24 - Running 'Factorial design specification'
Mapping files                           :                        ...done
Design configuration                    :                        ...done
Saving SPM configuration                :               ...SPM.mat saved
Design reporting                        :                        ...done
Completed                               :          11:21:24 - 03/05/2024
03-May-2024 11:21:24 - Done    'Factorial design specification'
03-May-2024 11:21:24 - Running 'Print figure'
Printing 'Graphics' figure to:
  /mnt/HD_jupiter/marcobarilari/datalad/analysis_high-res_BLAM_biMotion_localizers/outputs/derivatives/bidspm-stats/derivatives/bidspm-groupStats/sub-ALL_task-visualLocalizer_space-IXI549Space_FWHM-6_conFWHM-6_contrast-static/task-visualLocalizer_space-IXI549Space_desc-beforeEstimation_designmatrix_001.png
03-May-2024 11:21:25 - Done    'Print figure'
03-May-2024 11:21:25 - Running 'Factorial design specification'
Mapping files                           :                        ...done
Design configuration                    :                        ...done
Saving SPM configuration                :               ...SPM.mat saved
Design reporting                        :                        ...done
Completed                               :          11:21:26 - 03/05/2024
03-May-2024 11:21:26 - Done    'Factorial design specification'
03-May-2024 11:21:26 - Running 'Print figure'
Printing 'Graphics' figure to:
  /mnt/HD_jupiter/marcobarilari/datalad/analysis_high-res_BLAM_biMotion_localizers/outputs/derivatives/bidspm-stats/derivatives/bidspm-groupStats/sub-ALL_task-visualLocalizer_space-IXI549Space_FWHM-6_conFWHM-6_contrast-motion/task-visualLocalizer_space-IXI549Space_desc-beforeEstimation_designmatrix_001.png
03-May-2024 11:21:27 - Done    'Print figure'
03-May-2024 11:21:27 - Running 'Factorial design specification'
Mapping files                           :                        ...done
Design configuration                    :                        ...done
Saving SPM configuration                :               ...SPM.mat saved
Design reporting                        :                        ...done
Completed                               :          11:21:27 - 03/05/2024
03-May-2024 11:21:27 - Done    'Factorial design specification'
03-May-2024 11:21:27 - Running 'Print figure'
Printing 'Graphics' figure to:
  /mnt/HD_jupiter/marcobarilari/datalad/analysis_high-res_BLAM_biMotion_localizers/outputs/derivatives/bidspm-stats/derivatives/bidspm-groupStats/sub-ALL_task-visualLocalizer_space-IXI549Space_FWHM-6_conFWHM-6_contrast-response/task-visualLocalizer_space-IXI549Space_desc-beforeEstimation_designmatrix_001.png
03-May-2024 11:21:28 - Done    'Print figure'
03-May-2024 11:21:28 - Running 'Factorial design specification'
Mapping files                           :                        ...done
Design configuration                    :                        ...done
Saving SPM configuration                :               ...SPM.mat saved
Design reporting                        :                        ...done
Completed                               :          11:21:28 - 03/05/2024
03-May-2024 11:21:28 - Done    'Factorial design specification'
03-May-2024 11:21:28 - Running 'Print figure'
Printing 'Graphics' figure to:
  /mnt/HD_jupiter/marcobarilari/datalad/analysis_high-res_BLAM_biMotion_localizers/outputs/derivatives/bidspm-stats/derivatives/bidspm-groupStats/sub-ALL_task-visualLocalizer_space-IXI549Space_FWHM-6_conFWHM-6_contrast-staticGtMotion/task-visualLocalizer_space-IXI549Space_desc-beforeEstimation_designmatrix_001.png
03-May-2024 11:21:29 - Done    'Print figure'
03-May-2024 11:21:29 - Running 'Factorial design specification'
Mapping files                           :                        ...done
Design configuration                    :                        ...done
Saving SPM configuration                :               ...SPM.mat saved
Design reporting                        :                        ...done
Completed                               :          11:21:30 - 03/05/2024
03-May-2024 11:21:30 - Done    'Factorial design specification'
03-May-2024 11:21:30 - Running 'Print figure'
Printing 'Graphics' figure to:
  /mnt/HD_jupiter/marcobarilari/datalad/analysis_high-res_BLAM_biMotion_localizers/outputs/derivatives/bidspm-stats/derivatives/bidspm-groupStats/sub-ALL_task-visualLocalizer_space-IXI549Space_FWHM-6_conFWHM-6_contrast-motionGtStatic/task-visualLocalizer_space-IXI549Space_desc-beforeEstimation_designmatrix_001.png
03-May-2024 11:21:30 - Done    'Print figure'
03-May-2024 11:21:30 - Running 'Model estimation'

SPM12: spm_spm (v7738)                             11:21:30 - 03/05/2024
========================================================================
Chunk   1/1                             :                        ...done
Spatial non-sphericity (over scans)     :                        ...done
Saving SPM.mat                          :                        ...done
Completed                               :          11:21:33 - 03/05/2024
Done
03-May-2024 11:21:33 - Done    'Model estimation'
03-May-2024 11:21:33 - Running 'MA: inspect goodness of fit'
03-May-2024 11:21:35 - Failed  'MA: inspect goodness of fit'
Index exceeds array bounds.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/MA_inspect_GoF.m" (???), function "MA_inspect_GoF" at line 283.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/MA_inspect_GoF.m" (???), function "MA_inspect_GoF" at line 155.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/batch_MA_inspect_GoF.m" (???), function "run_module" at line 66.

03-May-2024 11:21:35 - Running 'MA: define model space'
03-May-2024 11:21:35 - Done    'MA: define model space'
03-May-2024 11:21:35 - Running 'MA: classical ICs (automatic)'

-> Subject 1 (1 out of 1):
   - Model GLM (1 out of 1) ... successful!

03-May-2024 11:21:38 - Done    'MA: classical ICs (automatic)'
03-May-2024 11:21:38 - Running 'Model review'
03-May-2024 11:21:39 - Done    'Model review'
03-May-2024 11:21:39 - Running 'Print figure'
Printing 'Graphics' figure to:
  /mnt/HD_jupiter/marcobarilari/datalad/analysis_high-res_BLAM_biMotion_localizers/outputs/derivatives/bidspm-stats/derivatives/bidspm-groupStats/sub-ALL_task-visualLocalizer_space-IXI549Space_FWHM-6_conFWHM-6_contrast-static/task-visualLocalizer_space-IXI549Space_desc-afterEstimation_designmatrix_001.png
03-May-2024 11:21:39 - Done    'Print figure'
03-May-2024 11:21:39 - Running 'Model estimation'

SPM12: spm_spm (v7738)                             11:21:39 - 03/05/2024
========================================================================
Chunk   1/1                             :                        ...done
Spatial non-sphericity (over scans)     :                        ...done
Saving SPM.mat                          :                        ...done
Completed                               :          11:21:42 - 03/05/2024
Done
03-May-2024 11:21:42 - Done    'Model estimation'
03-May-2024 11:21:42 - Running 'MA: inspect goodness of fit'
03-May-2024 11:21:43 - Failed  'MA: inspect goodness of fit'
Index exceeds array bounds.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/MA_inspect_GoF.m" (???), function "MA_inspect_GoF" at line 283.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/MA_inspect_GoF.m" (???), function "MA_inspect_GoF" at line 155.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/batch_MA_inspect_GoF.m" (???), function "run_module" at line 66.

03-May-2024 11:21:43 - Running 'MA: define model space'
03-May-2024 11:21:44 - Done    'MA: define model space'
03-May-2024 11:21:44 - Running 'MA: classical ICs (automatic)'

-> Subject 1 (1 out of 1):
   - Model GLM (1 out of 1) ... successful!

03-May-2024 11:21:47 - Done    'MA: classical ICs (automatic)'
03-May-2024 11:21:47 - Running 'Model review'
03-May-2024 11:21:47 - Done    'Model review'
03-May-2024 11:21:47 - Running 'Print figure'
Printing 'Graphics' figure to:
  /mnt/HD_jupiter/marcobarilari/datalad/analysis_high-res_BLAM_biMotion_localizers/outputs/derivatives/bidspm-stats/derivatives/bidspm-groupStats/sub-ALL_task-visualLocalizer_space-IXI549Space_FWHM-6_conFWHM-6_contrast-motion/task-visualLocalizer_space-IXI549Space_desc-afterEstimation_designmatrix_001.png
03-May-2024 11:21:48 - Done    'Print figure'
03-May-2024 11:21:48 - Running 'Model estimation'

SPM12: spm_spm (v7738)                             11:21:48 - 03/05/2024
========================================================================
Chunk   1/1                             :                        ...done
Spatial non-sphericity (over scans)     :                        ...done
Saving SPM.mat                          :                        ...done
Completed                               :          11:21:50 - 03/05/2024
Done
03-May-2024 11:21:50 - Done    'Model estimation'
03-May-2024 11:21:50 - Running 'MA: inspect goodness of fit'
03-May-2024 11:21:51 - Failed  'MA: inspect goodness of fit'
Index exceeds array bounds.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/MA_inspect_GoF.m" (???), function "MA_inspect_GoF" at line 283.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/MA_inspect_GoF.m" (???), function "MA_inspect_GoF" at line 155.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/batch_MA_inspect_GoF.m" (???), function "run_module" at line 66.

03-May-2024 11:21:51 - Running 'MA: define model space'
03-May-2024 11:21:51 - Done    'MA: define model space'
03-May-2024 11:21:52 - Running 'MA: classical ICs (automatic)'

-> Subject 1 (1 out of 1):
   - Model GLM (1 out of 1) ... successful!

03-May-2024 11:21:54 - Done    'MA: classical ICs (automatic)'
03-May-2024 11:21:54 - Running 'Model review'
03-May-2024 11:21:54 - Done    'Model review'
03-May-2024 11:21:54 - Running 'Print figure'
Printing 'Graphics' figure to:
  /mnt/HD_jupiter/marcobarilari/datalad/analysis_high-res_BLAM_biMotion_localizers/outputs/derivatives/bidspm-stats/derivatives/bidspm-groupStats/sub-ALL_task-visualLocalizer_space-IXI549Space_FWHM-6_conFWHM-6_contrast-response/task-visualLocalizer_space-IXI549Space_desc-afterEstimation_designmatrix_001.png
03-May-2024 11:21:55 - Done    'Print figure'
03-May-2024 11:21:55 - Running 'Model estimation'

SPM12: spm_spm (v7738)                             11:21:55 - 03/05/2024
========================================================================
Chunk   1/1                             :                        ...done
Spatial non-sphericity (over scans)     :                        ...done
Saving SPM.mat                          :                        ...done
Completed                               :          11:21:58 - 03/05/2024
Done
03-May-2024 11:21:58 - Done    'Model estimation'
03-May-2024 11:21:58 - Running 'MA: inspect goodness of fit'
03-May-2024 11:21:59 - Failed  'MA: inspect goodness of fit'
Index exceeds array bounds.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/MA_inspect_GoF.m" (???), function "MA_inspect_GoF" at line 283.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/MA_inspect_GoF.m" (???), function "MA_inspect_GoF" at line 155.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/batch_MA_inspect_GoF.m" (???), function "run_module" at line 66.

03-May-2024 11:21:59 - Running 'MA: define model space'
03-May-2024 11:21:59 - Done    'MA: define model space'
03-May-2024 11:21:59 - Running 'MA: classical ICs (automatic)'

-> Subject 1 (1 out of 1):
   - Model GLM (1 out of 1) ... successful!

03-May-2024 11:22:02 - Done    'MA: classical ICs (automatic)'
03-May-2024 11:22:02 - Running 'Model review'
03-May-2024 11:22:02 - Done    'Model review'
03-May-2024 11:22:02 - Running 'Print figure'
Printing 'Graphics' figure to:
  /mnt/HD_jupiter/marcobarilari/datalad/analysis_high-res_BLAM_biMotion_localizers/outputs/derivatives/bidspm-stats/derivatives/bidspm-groupStats/sub-ALL_task-visualLocalizer_space-IXI549Space_FWHM-6_conFWHM-6_contrast-staticGtMotion/task-visualLocalizer_space-IXI549Space_desc-afterEstimation_designmatrix_001.png
03-May-2024 11:22:03 - Done    'Print figure'
03-May-2024 11:22:03 - Running 'Model estimation'

SPM12: spm_spm (v7738)                             11:22:03 - 03/05/2024
========================================================================
Chunk   1/1                             :                        ...done
Spatial non-sphericity (over scans)     :                        ...done
Saving SPM.mat                          :                        ...done
Completed                               :          11:22:06 - 03/05/2024
Done
03-May-2024 11:22:06 - Done    'Model estimation'
03-May-2024 11:22:06 - Running 'MA: inspect goodness of fit'
03-May-2024 11:22:07 - Failed  'MA: inspect goodness of fit'
Index exceeds array bounds.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/MA_inspect_GoF.m" (???), function "MA_inspect_GoF" at line 283.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/MA_inspect_GoF.m" (???), function "MA_inspect_GoF" at line 155.
In file "/home/marcobarilari/data/tools/spm12/toolbox/MACS/batch_MA_inspect_GoF.m" (???), function "run_module" at line 66.

03-May-2024 11:22:07 - Running 'MA: define model space'
03-May-2024 11:22:07 - Done    'MA: define model space'
03-May-2024 11:22:07 - Running 'MA: classical ICs (automatic)'

-> Subject 1 (1 out of 1):
   - Model GLM (1 out of 1) ... successful!

03-May-2024 11:22:10 - Done    'MA: classical ICs (automatic)'
03-May-2024 11:22:10 - Running 'Model review'
03-May-2024 11:22:10 - Done    'Model review'
03-May-2024 11:22:10 - Running 'Print figure'
Printing 'Graphics' figure to:
  /mnt/HD_jupiter/marcobarilari/datalad/analysis_high-res_BLAM_biMotion_localizers/outputs/derivatives/bidspm-stats/derivatives/bidspm-groupStats/sub-ALL_task-visualLocalizer_space-IXI549Space_FWHM-6_conFWHM-6_contrast-motionGtStatic/task-visualLocalizer_space-IXI549Space_desc-afterEstimation_designmatrix_001.png
03-May-2024 11:22:11 - Done    'Print figure'
The following modules did not run:
Failed: MA: inspect goodness of fit
Failed: MA: inspect goodness of fit
Failed: MA: inspect goodness of fit
Failed: MA: inspect goodness of fit
Failed: MA: inspect goodness of fit


[11:22:11] bidspm - INFO				
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error message)
------------------ 
Running job #6
------------------

 Error matlabbatch:run:jobfailederr occurred:
	- Error in MATLABbatch system
		line 0 in 

ERROR LOG SAVED:
	/mnt/HD_jupiter/marcobarilari/datalad/analysis_high-res_BLAM_biMotion_localizers/outputs/derivatives/error_logs/error_2024-05-03T11-22.log
Use it when opening an issue:
	https://github.com/cpp-lln-lab/bidspm/issues/new/choose.

Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as
displayed in this error message)
------------------
Running job #6
------------------


Anything else?

No response

@marcobarilari marcobarilari added the bug 🐛 Something isn't working label May 3, 2024
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@marcobarilari
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@marcobarilari
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Any pointer would be very helpful. Thanks!

@FioritoAnna
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Hi! I have the same error message, did you find a solution?
Thanks,
Anna

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