TypeError: 'NoneType' object is not iterable

[vogelbac]

Hey I want to start Fitlins created the model but got the error TypeError: 'NoneType' object is not iterable

I am using the docker container :latest
this is the command I use:
sudo docker run --rm -it -v /home/g0rella/Desktop/SFB:/bids:ro -v /home/g0rella/Desktop/SFB/derivatives/fmriprep:/prep:ro -v /home/g0rella/Desktop/SFB/derivatives:/out poldracklab/fitlins:latest /bids /out run -d /prep --model models/model-001_smdl.json --participant-label sub-01

this is the model (model-001_smdl.json) I use:

{
"Name": "two_condition",
"Description": "A simple, two-condition contrast",
"Input": {
"task": "face"
},
"Steps": [
{
"Level": "Run",
"Transformations":[

	    {
	      "Name": "Factor",
	      "Inputs": ["trial_type"]
	    },
	    {
	      "Name": "Convolve",
	      "Model": "spm",
	      "Inputs": ["trial_type.face_fear", "trial_type.face_happy","trial_type.fixation_cross"]
	    }
  	
  	],
  
  "Model":{
  "X": [
    "trial_type.face_fear",
           "trial_type.face_happy",
           "trial_type.fixation_cross",
           "framewise_displacement",
           "trans_x",
           "trans_y",
           "trans_z",
           "rot_x",
           "rot_y",
           "rot_z",
           "a_comp_cor_00",
           "a_comp_cor_01",
           "a_comp_cor_02",
           "a_comp_cor_03",
           "a_comp_cor_04",
           "a_comp_cor_05"]
      },
      "DummyContrasts": {
    "Conditions": ["trial_type.face_fear", "trial_type.face_happy", "trial_type.fixation_cross"],
    "Type": "t"
    },
  "Contrasts": [
    {
      "Name": "fear_vs_fixation",
      "ConditionList": ["trial_type.face_fear", "trial_type.fixation_cross"],
      "Type": "t",
      "Weights": [1, -1]
    }
  ]
},
{
  "Level": "Dataset",
  "DummyContrasts": {
  "Conditions": ["fear_vs_fixation"],
    	"Type": "t"
  		}
  }

]
}

[effigies]

Hi, can you show the traceback of the error? And at a guess, this might be an issue with an invalid dataset_description.json in either your raw or derivative dataset.

[vogelbac]

For sure here is the traceback. For test reasons I used heudiconv to convert the DICOM data into BIDS and let the dataset_description.json as it was created. After running fmriprep I also let the dataset_description.json at it was. But then an error raised to add "PipelineDescription":{"Name":"Example pipeline"}. So I added this into the fmriprep dataset description. I hope this helps

sudo docker run --rm -it -v /home/g0rella/Desktop/SFB:/bids:ro -v /home/g0rella/Desktop/SFB/derivatives/fmriprep:/prep:ro -v /home/g0rella/Desktop/SFB/derivatives:/out poldracklab/fitlins:latest /bids /out run -d /prep --model models/model-001_smdl.json --participant-label sub-01
Captured warning (<class 'FutureWarning'>): Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.
220202-09:06:46,5 nipype.utils WARNING:
A newer version (1.7.0) of nipy/nipype is available. You are using 1.6.1
220202-09:06:53,816 nipype.workflow WARNING:
Storing result file without outputs
220202-09:06:53,816 nipype.workflow WARNING:
[Node] Error on "fitlins_wf.loader" (/tmp/tmphu_g7ngp/fitlins_wf/loader)
220202-09:06:54,167 nipype.workflow ERROR:
Node loader failed to run on host e93617da0a13.
220202-09:06:54,168 nipype.workflow ERROR:
Saving crash info to /work/crash-20220202-090654-neuro-loader-89ac0778-5d54-4a9e-b60e-6232f624f8c5.txt
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 148, in init
mp_context=mp_context,
TypeError: init() got an unexpected keyword argument 'initializer'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/fitlins/interfaces/bids.py", line 221, in _run_interface
analysis.setup(drop_na=False, **selectors)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/analysis.py", line 104, in setup
self.finalize(**selectors)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/analysis.py", line 112, in finalize
step.setup(input_contrasts, **kwargs)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/analysis.py", line 282, in setup
colls = tm.TransformerManager().transform(coll, self.transformations)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/transformations/base.py", line 458, in transform
func(collection, cols, **kwargs)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/transformations/base.py", line 96, in new
t._setup(collection, variables, *args, **kwargs)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/transformations/base.py", line 123, in _setup
self._expand_variable_groups()
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/transformations/base.py", line 131, in _expand_variable_groups
variables = [groups[v] if v in groups else [v] for v in self.variables]
TypeError: 'NoneType' object is not iterable

220202-09:06:56,163 nipype.workflow ERROR:
could not run node: fitlins_wf.loader
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/neuro/bin/fitlins", line 8, in
sys.exit(main())
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/fitlins/cli/run.py", line 294, in main
sys.exit(run_fitlins(sys.argv[1:]))
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/fitlins/cli/run.py", line 286, in run_fitlins
analysis.setup(**selectors)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/analysis.py", line 104, in setup
self.finalize(**selectors)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/analysis.py", line 112, in finalize
step.setup(input_contrasts, **kwargs)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/analysis.py", line 282, in setup
colls = tm.TransformerManager().transform(coll, self.transformations)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/transformations/base.py", line 458, in transform
func(collection, cols, **kwargs)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/transformations/base.py", line 96, in new
t._setup(collection, variables, *args, **kwargs)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/transformations/base.py", line 123, in _setup
self._expand_variable_groups()
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/transformations/base.py", line 131, in _expand_variable_groups
variables = [groups[v] if v in groups else [v] for v in self.variables]
TypeError: 'NoneType' object is not iterable