anibalsolon
commented
6 years ago @rattmowe it is a known issue for CPAC 1.1.0, that is going to be fixed in the next CPAC release. Meanwhile, in order to run this version, you may disable the quality control interface.
In order to do this, you need to download the default pipeline from: https://raw.githubusercontent.com/BIDS-Apps/CPAC/master/default_pipeline.yaml
Change this file, setting the flag generateQualityControlImages to [0]
Move this pipeline config to a folder, such as /home/matt/Documents/Projects/BIDS/cpac
Run the docker image, binding this new folder to the container and adding the pipeline argument:
docker run -i --rm -v /tmp:/scratch -v /home/matt/Documents/Projects/BIDS/cpac:/cpac_config -v /home/matt/Documents/Projects/BIDS/ds005:/bids_dataset -v /home/matt/outputs:/outputs bids/cpac /bids_dataset /outputs participant --participant_label 01 --pipeline_file /cpac_config/default_pipeline.yaml(it assumes that your pipeline config is default_pipeline.yaml)
Sorry for this inconvenient, we are releasing soon the new version with this fix and new analysis. Please let me know if it works or if you have more questions.
sgiavasis
Docker command used (directly implementing the participant level execution command from README):
docker run -i --rm -v /tmp:/scratch -v /home/matt/Documents/Projects/BIDS/ds005:/bids_dataset -v /home/matt/outputs:/outputs bids/cpac /bids_dataset /outputs participant --participant_label 01
Output:
Namespace(analysis_level='participant', anat_select_string=None, aws_config_input_creds=None, aws_data_input_creds=None, aws_output_creds=None, bids_dir='/bids_dataset', bids_validator_config=None, data_config_file=None, disable_file_logging=False, mem_gb=None, mem_mb=None, n_cpus='1', output_dir='/outputs', participant_label=['01'], participant_ndx=None, pipeline_file='/cpac_resources/default_pipeline.yaml', save_working_dir=False, skip_bids_validator=False)
Running BIDS validator 1: Invalid JSON file. The file is not formatted according the schema. (code: 55 - JSON_SCHEMA_VALIDATION_ERROR) ./dataset_description.json Evidence: .ReferencesAndLinks should be array
Running C-PAC on ['01']
Number of participants to run in parallel: 1 Input directory: /bids_dataset Output directory: /outputs/output Working directory: /scratch/working Crash directory: /outputs/crash Log directory: /outputs/log Remove working directory: True Available memory: 6.0 (GB) Available threads: 1 Number of threads for ANTs: 1 args.aws_data_input_creds None Checking participants.tsv file for site information: /bids_dataset/participants.tsv No site information found in the participants.tsv file.
[!] WARNING: Duplicate site-participant-session entry found in your input data directory!
Duplicate sets:
{'subject_id': '01', 'anat': '/bids_dataset/sub-01/anat/sub-01_T1w.nii.gz', 'site': 'site-1', 'unique_id': 'ses-1'}
{'subject_id': '01', 'anat': '/bids_dataset/sub-01/anat/sub-01_T1w.nii.gz', 'site': 'site-1', 'unique_id': 'ses-1'}
Only adding the first one to the data configuration file.
Starting participant level processing strategy_entries: [['_compcor_ncomponents_5_selector_pc10.linear1.wm0.global1.motion1.quadratic1.gm0.compcor1.csf1.ncomponents_5_selector_pc10.linear1.wm0.global0.motion1.quadratic1.gm0.compcor1.csf1', '_target_angle_deg_90', '_threshold_0.5']]
/usr/local/miniconda/lib/python2.7/site-packages/CPAC/pipeline/cpac_pipeline.py:201: UserWarning: Boolean Series key will be reindexed to match DataFrame index. outputs_native_nonsmooth = list(keys[keys['Optional outputs: Native space'] == 'yes'][keys['Optional outputs: Non-smoothed'] == 'yes'][keys['Multiple outputs'] != 'yes']['Resource']) /usr/local/miniconda/lib/python2.7/site-packages/CPAC/pipeline/cpac_pipeline.py:202: UserWarning: Boolean Series key will be reindexed to match DataFrame index. outputs_native_nonsmooth_mult = list(keys[keys['Optional outputs: Native space'] == 'yes'][keys['Optional outputs: Non-smoothed'] == 'yes'][keys['Multiple outputs'] == 'yes']['Resource']) /usr/local/miniconda/lib/python2.7/site-packages/CPAC/pipeline/cpac_pipeline.py:203: UserWarning: Boolean Series key will be reindexed to match DataFrame index. outputs_template_nonsmooth = list(keys[keys['Space'] == 'template'][keys['Optional outputs: Non-smoothed'] == 'yes'][keys['Multiple outputs'] != 'yes']['Resource']) /usr/local/miniconda/lib/python2.7/site-packages/CPAC/pipeline/cpac_pipeline.py:204: UserWarning: Boolean Series key will be reindexed to match DataFrame index. outputs_template_nonsmooth_mult = list(keys[keys['Space'] == 'template'][keys['Optional outputs: Non-smoothed'] == 'yes'][keys['Multiple outputs'] == 'yes']['Resource']) /usr/local/miniconda/lib/python2.7/site-packages/CPAC/pipeline/cpac_pipeline.py:207: UserWarning: Boolean Series key will be reindexed to match DataFrame index. outputs_native_smooth = list(keys[keys['Space'] != 'template'][keys['Derivative'] == 'yes'][keys['Optional outputs: Non-smoothed'] != 'yes']['Resource']) /usr/local/miniconda/lib/python2.7/site-packages/CPAC/pipeline/cpac_pipeline.py:210: UserWarning: Boolean Series key will be reindexed to match DataFrame index. outputs_template_smooth = list(keys[keys['Space'] == 'template'][keys['Derivative'] == 'yes'][keys['Optional outputs: Non-smoothed'] != 'yes']['Resource']) /usr/local/miniconda/lib/python2.7/site-packages/CPAC/pipeline/cpac_pipeline.py:215: UserWarning: Boolean Series key will be reindexed to match DataFrame index. outputs_template_raw = list(keys[keys['Space'] == 'template'][keys['Multiple outputs'] != 'yes'][keys['Optional outputs: Raw scores'] == 'yes']['Resource']) /usr/local/miniconda/lib/python2.7/site-packages/CPAC/pipeline/cpac_pipeline.py:216: UserWarning: Boolean Series key will be reindexed to match DataFrame index. outputs_template_raw_mult = list(keys[keys['Space'] == 'template'][keys['Multiple outputs'] == 'yes'][keys['Optional outputs: Raw scores'] == 'yes']['Resource']) /usr/local/miniconda/lib/python2.7/site-packages/CPAC/pipeline/cpac_pipeline.py:220: UserWarning: Boolean Series key will be reindexed to match DataFrame index. outputs_average = list(keys[keys['Calculate averages'] == 'yes'][keys['Multiple outputs'] != 'yes']['Resource']) /usr/local/miniconda/lib/python2.7/site-packages/CPAC/pipeline/cpac_pipeline.py:221: UserWarning: Boolean Series key will be reindexed to match DataFrame index. outputs_average_mult = list(keys[keys['Calculate averages'] == 'yes'][keys['Multiple outputs'] == 'yes']['Resource']) 180731-15:34:39,644 workflow INFO: VERSION: CPAC 1.1.0
Setting maximum number of cores per participant to 1 Setting number of participants at once to 1 Setting OMP_NUM_THREADS to 1 Setting MKL_NUM_THREADS to 1 Setting ANTS/ITK thread usage to 1
Maximum potential number of cores that might be used during this run: 1
++ 3dcalc: AFNI version=AFNI_18.1.18 (May 25 2018) [64-bit] ++ Authored by: A cast of thousands 180731-15:34:39,731 interface WARNING: afni_vcheck executable not found. 180731-15:34:40,70 workflow INFO: connected input to slc 180731-15:34:40,70 workflow INFO: connected TR 180731-15:34:40,70 workflow INFO: slice timing pattern ['Use NIFTI Header'] 180731-15:34:40,70 workflow INFO: finished connecting slice timing pattern 180731-15:34:40,93 workflow INFO: infile rest connected 180731-15:34:40,110 workflow INFO: Warning key movement_parameters already exists in resource pool, replacing with (resting_preproc_01_ses-1.fristons_parameter_model_0, 'outputspec.movement_file') 180731-15:34:40,161 workflow INFO: Warning key mean_functional_in_anat already exists in resource pool, replacing with (resting_preproc_01_ses-1.func_to_anat_bbreg_0, 'outputspec.anat_func') 180731-15:34:40,161 workflow INFO: Warning key functional_to_anat_linear_xfm already exists in resource pool, replacing with (resting_preproc_01_ses-1.func_to_anat_bbreg_0, 'outputspec.func_to_anat_linear_xfm') 180731-15:34:41,444 workflow INFO: Using AFNI centrality function 180731-15:34:41,449 workflow INFO: Using AFNI LFCD function 180731-15:34:42,440 workflow INFO:
Pipeline building completed.
180731-15:34:42,641 workflow INFO: no node for output: 180731-15:34:42,641 workflow INFO: sca_roi_files_to_standard [!] Connection of QA montages workflow for sca_roi_files_to_standard has failed.
Error: 'sca_roi_files_to_standard' 180731-15:34:42,641 workflow INFO: no node for output: 180731-15:34:42,641 workflow INFO: sca_roi_files_to_standard_smooth [!] Connection of QA montages workflow for sca_roi_files_to_standard_smooth has failed.
Error: 'sca_roi_files_to_standard_smooth' 180731-15:34:42,641 workflow INFO: no node for output: 180731-15:34:42,642 workflow INFO: sca_roi_files_to_standard_smooth_fisher_zstd [!] Connection of QA montages workflow for sca_roi_files_to_standard_smooth_fisher_zstd has failed.
Error: 'sca_roi_files_to_standard_smooth_fisher_zstd' 180731-15:34:42,705 workflow INFO:
ERROR: QC - unable to get resources for SNR plot
Error name: cpac_pipeline_0051
Process Process-1: Traceback (most recent call last): File "/usr/local/miniconda/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/local/miniconda/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/usr/local/miniconda/lib/python2.7/site-packages/CPAC/pipeline/cpac_pipeline.py", line 4342, in prep_workflow workflow.connect(preproc, out_file, stddev, 'func') File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 233, in connect infostr)) Exception: Some connections were not found Module func_preproc_automask_0 has no output called outputspec.output_image