shnizzedy / c-pac

Configurable Pipeline for the Analysis of Connectomes

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c-pac's Issues

🚀 Run rest_test_CPACv1.6.2_nuis1-3a.yml without errors

• 🔗 rest_test_CPACv1.6.2_nuis1-3a.yml

📧 atlas in cifti format

We're trying to use a new subcortical atlas that's incorporated into a gordon cortex atlas. It's available only in a cifti format. Do you have any suggestions for how to use this with cpac, particularly as it's in cifti format?

2. how to use the gordon-tian atlas we identified, which is not an existing atlas in CPAC and is in cifti format.

🐛 "OSError: Duplicate node name"

Describe the bug

Trying to test FCP-INDI#1524 (cpac-singularity-image.simg) with prelim_forks_ses_test.yml, I get

Connecting nuisance_regression...

Traceback (most recent call last):
  File "/code/run.py", line 672, in <module>
    test_config = 1 if args.analysis_level == "test_config" else 0
  File "/code/CPAC/pipeline/cpac_runner.py", line 549, in run
    p_name, plugin, plugin_args, test_config)
  File "/code/CPAC/pipeline/cpac_pipeline.py", line 395, in run_workflow
    subject_id, sub_dict, c, p_name, num_ants_cores
  File "/code/CPAC/pipeline/cpac_pipeline.py", line 1261, in build_workflow
    wf = connect_pipeline(wf, cfg, rpool, pipeline_blocks)
  File "/code/CPAC/pipeline/cpac_pipeline.py", line 976, in connect_pipeline
    wf = nb.connect_block(wf, cfg, rpool)
  File "/code/CPAC/pipeline/engine.py", line 1163, in connect_block
    pipe_x, opt)
  File "/code/CPAC/nuisance/nuisance.py", line 2141, in nuisance_regression_complete
    wf.connect(node, out, regressors, 'inputspec.functional_file_path')
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py", line 158, in connect
    self._check_nodes(newnodes)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py", line 766, in _check_nodes
    raise IOError('Duplicate node name "%s" found.' % node.name)
OSError: Duplicate node name "nuisance_regressors_2-aCompCor-no-GSR-no-spike-regression_128" found.

C-PAC seems to be duplicating at least that one regressor somehow?

To Reproduce
Steps to reproduce the behavior:

singularity run \
  -B /$output:/outputs \
  -B ${BIDS_DIR}:/bids_dataset \
  -B ${CPAC_DIR}:/code \
  -B ${DATA_CONFIG}:/data_config \
  -B ${CPAC_DIR}/CPAC/resources/configs:${CPAC_DIR}/CPAC/resources/configs \
  -B /tmp:/scratch -B /media/ebs/Columbia_Nim/configs:/configs \
  cpac-singularity-image.simg /bids_dataset /outputs participant \
  --data_config_file ${DATA_CONFIG_FILE} \
  --pipeline_file /configs/prelim_forks_ses_test.yml \
  --mem_gb 100 \
  --participant_label ${PARTICIPANT}

Versions

• C-PAC: 1.8.1-dev @ FCP-INDI@38b295f
• Container Platform :
  • Singularity: 3.7.2

Additional context

The regressor section of the pipeline file:

nuisance_corrections: 
  2-nuisance_regression: 
    run: [On]
    Regressors: 
      #1: aCompCor, GSR, no spike regression
      - Name: "1-aCompCor-GSR-no-spike-regression"
        Motion:
          include_delayed: true
          include_squared: true
          include_delayed_squared: true
        aCompCor:
          summary:
            method: DetrendPC
            components: 5
          tissues:
            - WhiteMatter
            - CerebrospinalFluid
          extraction_resolution: 2
        GlobalSignal:
          summary: Mean
        PolyOrt:
          degree: 2
        Bandpass:
          bottom_frequency: 0.01
          top_frequency: 0.1
      #2 aCompCor, no GSR, no spike regression
      - Name: "2-aCompCor-no-GSR-no-spike-regression"
        Motion:
          include_delayed: true
          include_squared: true
          include_delayed_squared: true
        aCompCor:
          summary:
            method: DetrendPC
            components: 5
          tissues:
            - WhiteMatter
            - CerebrospinalFluid
          extraction_resolution: 2
        PolyOrt:
          degree: 2
        Bandpass:
          bottom_frequency: 0.01
          top_frequency: 0.1
      #3 No aCompCor, GSR, no spike regression
      - Name: "3-No-aCompCor-GSR-no-spike-regression"
        Motion:
          include_delayed: true
          include_squared: true
          include_delayed_squared: true
        GlobalSignal:
          summary: Mean
        PolyOrt:
          degree: 2
        Bandpass:
          bottom_frequency: 0.01
          top_frequency: 0.1
      #4 No aCompCor, no GSR, no spike regression
      - Name: "4-No-aCompCor-no-GSR-no-spike-regression"
        Motion:
          include_delayed: true
          include_squared: true
          include_delayed_squared: true
        PolyOrt:
          degree: 2
        Bandpass:
          bottom_frequency: 0.01
          top_frequency: 0.1
      #5: aCompCor, GSR, spike regression
      - Name: "5-aCompCor-GSR-spike-regression"
        Motion:
          include_delayed: true
          include_squared: true
          include_delayed_squared: true
        aCompCor:
          summary:
            method: DetrendPC
            components: 5
          tissues:
            - WhiteMatter
            - CerebrospinalFluid
          extraction_resolution: 2
        GlobalSignal:
          summary: Mean
        PolyOrt:
          degree: 2
        Bandpass:
          bottom_frequency: 0.01
          top_frequency: 0.1
        Censor:
            method: SpikeRegression
            thresholds:
              - type: FD_J
                value: 0.2
            number_of_previous_trs_to_censor: 0
            number_of_subsequent_trs_to_censor: 0
      #6 aCompCor, no GSR, spike regression
      - Name: "6-aCompCor-no-GSR-spike-regression"
        Motion:
          include_delayed: true
          include_squared: true
          include_delayed_squared: true
        aCompCor:
          summary:
            method: DetrendPC
            components: 5
          tissues:
            - WhiteMatter
            - CerebrospinalFluid
          extraction_resolution: 2
        PolyOrt:
          degree: 2
        Bandpass:
          bottom_frequency: 0.01
          top_frequency: 0.1
        Censor:
            method: SpikeRegression
            thresholds:
              - type: FD_J
                value: 0.2
            number_of_previous_trs_to_censor: 0
            number_of_subsequent_trs_to_censor: 0
      #7 No aCompCor, GSR, spike regression
      - Name: "7-No-aCompCor-GSR-spike-regression"
        Motion:
          include_delayed: true
          include_squared: true
          include_delayed_squared: true
        GlobalSignal:
          summary: Mean
        PolyOrt:
          degree: 2
        Bandpass:
          bottom_frequency: 0.01
          top_frequency: 0.1
        Censor:
            method: SpikeRegression
            thresholds:
              - type: FD_J
                value: 0.2
            number_of_previous_trs_to_censor: 0
            number_of_subsequent_trs_to_censor: 0
      #8 No aCompCor, no GSR, spike regression
      - Name: "8-No-aCompCor-no-GSR-spike-regression"
        Motion:
          include_delayed: true
          include_squared: true
          include_delayed_squared: true
        PolyOrt:
          degree: 2
        Bandpass:
          bottom_frequency: 0.01
          top_frequency: 0.1
        Censor:
            method: SpikeRegression
            thresholds:
              - type: FD_J
                value: 0.2
            number_of_previous_trs_to_censor: 0
            number_of_subsequent_trs_to_censor: 0

Re-re-run sub-NDARZP630WYL multicore on CUBIC

🕵️ Determine cause of fewer timepoints than regressors

2. For diff-proj-SB151-lessmotion, I'm not sure why so much is getting censored. The problem here is that so much gets censored that there are fewer timepoints left than regressors. I'm running this one by the rest of the team to see if they have any ideas.

🕵️ `OSError: [Errno 5] Input/output error`

C-PAC v.1.6.2 SameFile Error and time point missmatch error

📧 C-PAC v.1.6.2 SameFile Error and time point missmatch error

Run sub-NDARZP630WYL linearly on CUBIC

Run sub-NDARZP630WYL on CNL server

🐛 `gen_motion_stats` not getting all necessary parameters

Describe the bug

C-PAC/CPAC/pipeline/cpac_pipeline.py

Lines 2202 to 2218 in 33e22b2

	if 'motion_params' not in strat:
	# skullstripping tool
	skullstrip_tool = strat.get('bold_masking_method')
	# motion correction reference
	motion_correct_ref = strat.get('motion_correction_ref')
	# motion correction tool
	motion_correct_tool = strat.get('motion_correction_method')
	gen_motion_stats = motion_power_statistics(
	name='gen_motion_stats_{0}_{1}_{2}_{3}'.format(skullstrip_tool,
	motion_correct_ref,
	motion_correct_tool,
	num_strat),
	motion_correct_tool=motion_correct_tool)

200606-00:00:33,108 nipype.workflow ERROR:
	 could not run node: resting_preproc_2014113_1.gen_motion_stats_None_None_None_0.calc_motion_parameters.b0

200606-00:00:33,108 nipype.workflow ERROR:
	 could not run node: resting_preproc_2014113_1.gen_motion_stats_None_None_None_0.calc_power_parameters.b0

200606-00:00:33,109 nipype.workflow ERROR:
	 could not run node: resting_preproc_2014113_1.gen_motion_stats_None_None_None_0.calculate_FDJ

Versions

• C-PAC: FCP-INDI@a9ae37e (Ⓢ 🐳)
• Container Platform :
  • Singularity: 2.5.2

Additional context
This may be fixed in FCP-INDI#1288