C-PAC v1.8.0 dev - rodent preconfig

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:

[x] 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]

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]

[x] 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

C-PAC Run Info


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

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']

C-PAC Run Info


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

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'

FCP-INDI / cpac_run_logs