C-PAC v1.8.0 dev - rodent preconfig

[HechengJin0]

02/22/2021 update

C-PAC Run Info

Description	monkey preconfig
Version	v1.8.0 dev
Container	fcpindi/c-pac dev-v1.8 28dd58f2c661
System	lisa

Results

Connecting coregistration...

Traceback (most recent call last):
  File "/code/run.py", line 677, 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 348, in run_workflow
    subject_id, sub_dict, c, p_name, num_ants_cores
  File "/code/CPAC/pipeline/cpac_pipeline.py", line 1067, in build_workflow
    wf = connect_pipeline(wf, cfg, rpool, pipeline_blocks)
  File "/code/CPAC/pipeline/cpac_pipeline.py", line 807, in connect_pipeline
    wf = nb.connect_block(wf, cfg, rpool)
  File "/code/CPAC/pipeline/engine.py", line 1092, in connect_block
    pipe_x, opt)
  File "/code/CPAC/registration/registration.py", line 2010, in coregistration
    node, out = strat_pool.get_data(["label-WM_probseg", "label-WM_mask"])
  File "/code/CPAC/pipeline/engine.py", line 269, in get_data
    return self.get(resource)['data']
  File "/code/CPAC/pipeline/engine.py", line 231, in get
    raise Exception("\n[!] C-PAC says: None of the listed "
Exception: 
[!] C-PAC says: None of the listed resources are in the resource pool:
['label-WM_probseg', 'label-WM_mask']

Developer note
Config:

  tissue_segmentation: 
    using: ['Template_Based']

    Template_Based: 
      template_for_segmentation: [EPI_Template]

func-to-anat coreg needs wm mask. none of ['label-WM_probseg', 'label-WM_mask'] is from EPI_Template based segmentation

solution: add 'space-bold_label-WM_mask'? see tissue_seg_EPI_template_based

Include:

• Run Command:

docker run --cpus "8" -m 4g --user id -u:id -g -i --rm --security-opt=apparmor:unconfined -v /data3/cnl/rodent/rodent_data_website/all_BIDS:/bids_dataset -v /data3/cnl/rodent/rodent_data_website/all:/data3/cnl/rodent/rodent_data_website/all -v /data3/cnl/rodent/cpac_run/output/rodent_0218_2021_cpac18_dev_preconfig:/outputs -v /tmp:/scratch -v /data3/cnl/rodent/template:/template fcpindi/c-pac:dev-v1.8 /bids_dataset /outputs participant --preconfig rodent --save_working_dir --n_cpus 16 --mem_gb 40 --participant_label [a ag150519a ag150520b]

• Pipeline Config (can drag file directly into issue)
  https://github.com/FCP-INDI/C-PAC/blob/develop_v1.8_convergence/CPAC/resources/configs/pipeline_config_rodent.yml
• Data Config (can drag file directly into issue)

Developers only:

• Default Pipeline Diff:

(print-out from cpac_pipe_diff.py)

• Screenshots of brain extraction and registration wireframe overlays from QC pages (if available):

screenshots here

• Node timing information:

(print-out from callback_log_time_parse.py)

• Extracted time series 1D and nuisance regressors 1D correlations against previous version or some benchmark (can use corr_two_1D.py but heatmaps or other visualizations are good too):

correlations here

[HechengJin0]

02/22/2018 8:10 PM update:

C-PAC Run Info

Description	rodent preconfig
Version	v1.8.0 dev
Container	fcpindi/c-pac dev-v1.8 7047f0be627c
System	lisa

Results

Connecting anatomical_init...

sm label: desc-preproc_T1w
sm label: desc-reorient_T1w
Connecting n4_bias_correction...

sm label: desc-preproc_T1w
Connecting brain_mask_fsl...

sm label: space-T1w_desc-brain_mask
Connecting brain_extraction...

sm label: desc-brain_T1w
Connecting register_ANTs_anat_to_template...

sm label: space-template_desc-brain_T1w
sm label: from-T1w_to-template_mode-image_xfm
sm label: from-template_to-T1w_mode-image_xfm
sm label: from-T1w_to-template_mode-image_desc-linear_xfm
sm label: from-template_to-T1w_mode-image_desc-linear_xfm
sm label: from-T1w_to-template_mode-image_desc-nonlinear_xfm
sm label: from-template_to-T1w_mode-image_desc-nonlinear_xfm
Connecting tissue_seg_EPI_template_based...

Connecting func_truncate...

sm label: desc-preproc_bold
Connecting func_reorient...

sm label: desc-preproc_bold
Connecting get_motion_ref...

sm label: motion-basefile
Connecting motion_correction...

sm label: desc-motion_bold
sm label: max-displacement
sm label: movement-parameters
sm label: coordinate-transformation
Connecting bold_mask_fsl...

sm label: space-bold_desc-brain_mask
Connecting bold_masking...

sm label: desc-brain_bold
Connecting calc_motion_stats...

sm label: framewise-displacement-power
sm label: framewise-displacement-jenkinson
sm label: dvars
sm label: power-params
sm label: motion-params
Connecting func_mean...

sm label: desc-mean_bold
Connecting func_normalize...

sm label: desc-brain_bold
sm label: space-bold_desc-brain_mask
Connecting coregistration_prep_mean...

sm label: bold_coreg_input
Connecting coregistration...

Traceback (most recent call last):
  File "/code/run.py", line 677, 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 348, in run_workflow
    subject_id, sub_dict, c, p_name, num_ants_cores
  File "/code/CPAC/pipeline/cpac_pipeline.py", line 1067, in build_workflow
    wf = connect_pipeline(wf, cfg, rpool, pipeline_blocks)
  File "/code/CPAC/pipeline/cpac_pipeline.py", line 807, in connect_pipeline
    wf = nb.connect_block(wf, cfg, rpool)
  File "/code/CPAC/pipeline/engine.py", line 1092, in connect_block
    pipe_x, opt)
  File "/code/CPAC/registration/registration.py", line 2016, in coregistration
    node, out = strat_pool.get_data(["label-WM_probseg", "label-WM_mask"])
  File "/code/CPAC/pipeline/engine.py", line 269, in get_data
    return self.get(resource)['data']
  File "/code/CPAC/pipeline/engine.py", line 231, in get
    raise Exception("\n[!] C-PAC says: None of the listed "
Exception: 
[!] C-PAC says: None of the listed resources are in the resource pool:
['label-WM_probseg', 'label-WM_mask']

[HechengJin0]

03/10/2021 11:30 AM update:

C-PAC Run Info

Description	rodent preconfig
Version	v1.8.0 dev
Container	fcpindi/c-pac dev-v1.8 0f5552fa26e2
System	lisa

Results

Connecting anatomical_init...

Connecting n4_bias_correction...

Connecting brain_mask_fsl...

Connecting brain_extraction...

Connecting register_ANTs_anat_to_template...

Connecting tissue_seg_EPI_template_based...

Connecting func_truncate...

Connecting func_reorient...

Connecting get_motion_ref...

Connecting motion_correction...

Connecting bold_mask_fsl...

Connecting bold_masking...

Connecting calc_motion_stats...

Connecting func_mean...

Connecting func_normalize...

Connecting coregistration_prep_mean...

Connecting register_ANTs_EPI_to_template...

Connecting tissue_seg_EPI_template_based...

Connecting nuisance_regression_EPItemplate...

Connecting transform_timeseries_to_EPItemplate...

Traceback (most recent call last):
  File "/code/run.py", line 677, 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 359, in run_workflow
    subject_id, sub_dict, c, p_name, num_ants_cores
  File "/code/CPAC/pipeline/cpac_pipeline.py", line 1132, in build_workflow
    wf = connect_pipeline(wf, cfg, rpool, pipeline_blocks)
  File "/code/CPAC/pipeline/cpac_pipeline.py", line 860, in connect_pipeline
    wf = nb.connect_block(wf, cfg, rpool)
  File "/code/CPAC/pipeline/engine.py", line 1144, in connect_block
    pipe_x, opt)
  File "/code/CPAC/registration/registration.py", line 2494, in warp_timeseries_to_EPItemplate
    mem_gb=2.5)
TypeError: apply_transform() got an unexpected keyword argument 'mem_gb'