app-C-PAC-brainlife.io v0.0.0.dev / C-PAC v1.7.2 - fmriprep-options

C-PAC Run Info


Description	https://github.com/FCP-INDI/cpac_run_logs/issues/3 with different data and newer C-PAC
Version	1.7.2
Container	Singularity
System	brainlife.io
Data Size	900 TRs (74 × 74 × 40)
Results	```Python End of subject workflow resting_preproc_sub-A00013809_ses-DS2 CPAC run complete: Pipeline configuration: cpac_fmriprep-options Subject workflow: resting_preproc_sub-A00013809_ses-DS2 Elapsed run time (minutes): 457.36562920014063 Timing information saved in /output/log/cpac_individual_timing_cpac_fmriprep-options.csv System time of start: 2020-11-18 15:47:21 System time of completion: 2020-11-18 23:24:39 ```

Include:

[x] Run Command:

anat/t1w:
  NKI: A00013809 / DS2 | DS2
func/task: 
  NKI: A00013809 / DS2 rest | DS2,rest,645
preconfig: fmriprep-options

[x] Pipeline Config: fmriprep-options
[x] Data Config: BIDS

Developers only:

[x] Default Pipeline Diff:

FSLDIR: ('/usr/share/fsl/5.0', 'FSLDIR')
parallelEnvironment: ('mpi_smp', 'cpac')
num_ants_threads: (4, 1)
s3Encryption: ([0], [1])
n4_bias_field_correction: (False, True)
acpc_align: (False, None)
acpc_brainsize: (150, None)
acpc_template_skull: ('/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm.nii.gz', None)
acpc_template_brain: ('None', None)
skullstrip_option: (['AFNI'], ['niworkflows-ants'])
bet_mask_boolean: (True, False)
resolution_for_anat: ('2mm', '1mm')
template_brain_only_for_anat: ('/usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz', '/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz')
template_skull_for_anat: ('/usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz', '/code/CPAC/resources/templates/mni_icbm152_t1_tal_nlin_asym_09c.nii')
ANTs_para_T1_registration: ([{'collapse-output-transforms': 0}, {'dimensionality': 3}, {'initial-moving-transform': {'initializationFeature': 0}}, {'transforms': [{'Rigid': {'gradientStep': 0.1, 'metric': {'type': 'MI', 'metricWeight': 1, 'numberOfBins': 32, 'samplingStrategy': 'Regular', 'samplingPercentage': 0.25}, 'convergence': {'iteration': '1000x500x250x100', 'convergenceThreshold': '1e-08', 'convergenceWindowSize': 10}, 'smoothing-sigmas': '3.0x2.0x1.0x0.0', 'shrink-factors': '8x4x2x1', 'use-histogram-matching': True}}, {'Affine': {'gradientStep': 0.1, 'metric': {'type': 'MI', 'metricWeight': 1, 'numberOfBins': 32, 'samplingStrategy': 'Regular', 'samplingPercentage': 0.25}, 'convergence': {'iteration': '1000x500x250x100', 'convergenceThreshold': '1e-08', 'convergenceWindowSize': 10}, 'smoothing-sigmas': '3.0x2.0x1.0x0.0', 'shrink-factors': '8x4x2x1', 'use-histogram-matching': True}}, {'SyN': {'gradientStep': 0.1, 'updateFieldVarianceInVoxelSpace': 3.0, 'totalFieldVarianceInVoxelSpace': 0.0, 'metric': {'type': 'CC', 'metricWeight': 1, 'radius': 4}, 'convergence': {'iteration': '100x100x70x20', 'convergenceThreshold': '1e-09', 'convergenceWindowSize': 15}, 'smoothing-sigmas': '3.0x2.0x1.0x0.0', 'shrink-factors': '6x4x2x1', 'use-histogram-matching': True, 'winsorize-image-intensities': {'lowerQuantile': 0.01, 'upperQuantile': 0.99}}}]}], [{'collapse-output-transforms': 1}, {'dimensionality': 3}, {'initial-moving-transform': {'initializationFeature': 0}}, {'transforms': [{'Rigid': {'gradientStep': 0.05, 'metric': {'type': 'MI', 'metricWeight': 1, 'numberOfBins': 32, 'samplingStrategy': 'Regular', 'samplingPercentage': 0.25}, 'convergence': {'iteration': '100x100', 'convergenceThreshold': '1e-06', 'convergenceWindowSize': 20}, 'smoothing-sigmas': '2.0x1.0vox', 'shrink-factors': '2x1', 'use-histogram-matching': True}}, {'Affine': {'gradientStep': 0.08, 'metric': {'type': 'MI', 'metricWeight': 1, 'numberOfBins': 32, 'samplingStrategy': 'Regular', 'samplingPercentage': 0.25}, 'convergence': {'iteration': '100x100', 'convergenceThreshold': '1e-06', 'convergenceWindowSize': 20}, 'smoothing-sigmas': '1.0x0.0vox', 'shrink-factors': '2x1', 'use-histogram-matching': True}}, {'SyN': {'gradientStep': 0.1, 'updateFieldVarianceInVoxelSpace': 3.0, 'totalFieldVarianceInVoxelSpace': 0.0, 'metric': {'type': 'CC', 'metricWeight': 1, 'radius': 4}, 'convergence': {'iteration': '100x70x50x20', 'convergenceThreshold': '1e-06', 'convergenceWindowSize': 10}, 'smoothing-sigmas': '3.0x2.0x1.0x0.0vox', 'shrink-factors': '8x4x2x1', 'use-histogram-matching': True, 'winsorize-image-intensities': {'lowerQuantile': 0.005, 'upperQuantile': 0.995}}}]}])
ref_mask: ('/usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz', '$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz')
regWithSkull: ([1], [0])
ANTs_prior_based_segmentation: ([0], None)
ANTs_prior_seg_template_brain_list: (['/monkey_seg/templates/JointLabelCouncil/MacaqueYerkes19_T1w_0.5mm/T1w_brain.nii.gz', '/monkey_seg/templates/JointLabelCouncil/J_Macaque_11mo_atlas_nACQ_194x252x160space_0.5mm/T1w_brain.nii.gz'], None)
ANTs_prior_seg_template_segmentation_list: (['/monkey_seg/templates/JointLabelCouncil/MacaqueYerkes19_T1w_0.5mm/Segmentation.nii.gz', '/monkey_seg/templates/JointLabelCouncil/J_Macaque_11mo_atlas_nACQ_194x252x160space_0.5mm/Segmentation.nii.gz'], None)
ANTs_prior_seg_CSF_label: (24, None)
ANTs_prior_seg_left_GM_label: (3, None)
ANTs_prior_seg_right_GM_label: (42, None)
ANTs_prior_seg_left_WM_label: (2, None)
ANTs_prior_seg_right_WM_label: (41, None)
seg_use_priors: (True, False)
seg_use_threshold: (['FSL-FAST Thresholding'], ['Customized Thresholding'])
seg_csf_use_erosion: (False, True)
brain_use_erosion: (False, True)
seg_wm_use_erosion: (False, True)
runMotionStatisticsFirst: ([0], [1])
motion_correction: (['3dvolreg'], ['mcflirt'])
motion_estimate_filter: ({'run': [False], 'filter_type': 'notch', 'filter_order': 4, 'breathing_rate_min': None, 'breathing_rate_max': None, 'center_frequency': None, 'filter_bandwidth': None, 'lowpass_cutoff': None}, None)
distortion_correction: (['None'], ['PhaseDiff', 'Blip'])
boundaryBasedRegistrationSchedule: ('/usr/share/fsl/5.0/etc/flirtsch/bbr.sch', '$FSLDIR/etc/flirtsch/bbr.sch')
n4_correct_func_reg_input: (False, None)
functionalMasking: (['AFNI'], ['FSL_AFNI'])
bold_bet_functional_mean_boolean: (False, None)
bold_bet_frac: (0.3, None)
bold_bet_mesh_boolean: (False, None)
bold_bet_outline: (False, None)
bold_bet_padding: (False, None)
bold_bet_radius: (0, None)
bold_bet_reduce_bias: (False, None)
bold_bet_remove_eyes: (False, None)
bold_bet_robust: (False, None)
bold_bet_skull: (False, None)
bold_bet_surfaces: (False, None)
bold_bet_threshold: (False, None)
bold_bet_vertical_gradient: (0.0, None)
resolution_for_func_preproc: ('3mm', '3.438mmx3.438mmx3.4mm')
resolution_for_func_derivative: ('3mm', '3.438mmx3.438mmx3.4mm')
template_for_resample: ('$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz', '/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz')
template_brain_only_for_func: ('/usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_func_preproc}_brain.nii.gz', '/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_res-02_T1w_reference.nii.gz')
template_skull_for_func: ('/usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_func_preproc}.nii.gz', '/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_res-02_T1w_reference.nii.gz')
identityMatrix: ('/usr/share/fsl/5.0/etc/flirtsch/ident.mat', '$FSLDIR/etc/flirtsch/ident.mat')
runNuisance: ([1], [0])
lateral_ventricles_mask: ('$FSLDIR/data/atlases/HarvardOxford/HarvardOxford-lateral-ventricles-thr25-2mm.nii.gz', 'None')
Regressors: ([{'Motion': {'include_delayed': True, 'include_squared': True, 'include_delayed_squared': True}, 'aCompCor': {'summary': {'method': 'DetrendPC', 'components': 5}, 'tissues': ['WhiteMatter', 'CerebrospinalFluid'], 'extraction_resolution': 2}, 'CerebrospinalFluid': {'summary': 'Mean', 'extraction_resolution': 2, 'erode_mask': True}, 'GlobalSignal': {'summary': 'Mean'}, 'PolyOrt': {'degree': 2}, 'Bandpass': {'bottom_frequency': 0.01, 'top_frequency': 0.1}}, {'Motion': {'include_delayed': True, 'include_squared': True, 'include_delayed_squared': True}, 'aCompCor': {'summary': {'method': 'DetrendPC', 'components': 5}, 'tissues': ['WhiteMatter', 'CerebrospinalFluid'], 'extraction_resolution': 2}, 'CerebrospinalFluid': {'summary': 'Mean', 'extraction_resolution': 2, 'erode_mask': True}, 'PolyOrt': {'degree': 2}, 'Bandpass': {'bottom_frequency': 0.01, 'top_frequency': 0.1}}], [{'Bandpass': {'bottom_frequency': 0.01, 'top_frequency': 0.1}, 'CerebrospinalFluid': {'erode_mask': False, 'summary': 'Mean', 'extraction_resolution': 2}, 'GlobalSignal': {'summary': 'Mean'}, 'Motion': {'include_delayed': True, 'include_delayed_squared': True, 'include_squared': True}, 'PolyOrt': {'degree': 2}, 'WhiteMatter': {'erode_mask': False, 'summary': 'Mean', 'extraction_resolution': 2}, 'aCompCor': {'summary': {'components': 5, 'filter': 'cosine', 'method': 'PC'}, 'tissues': ['WhiteMatter', 'CerebrospinalFluid'], 'extraction_resolution': 2}, 'tCompCor': {'summary': {'components': 5, 'filter': 'cosine', 'method': 'PC'}, 'threshold': '5PCT', 'erode_mask_mm': True, 'degree': 2}}])
runROITimeseries: ([1], [0])
runSCA: ([1], [0])
runVMHC: ([1], [0])
runALFF: ([1], [0])
runReHo: ([1], [0])
runNetworkCentrality: ([1], [0])
templateSpecificationFile: ('/cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz', 's3://fcp-indi/resources/cpac/resources/mask-thr50-3mm.nii.gz')
eigWeightOptions: ([False, True], [True, True])
lfcdCorrelationThresholdOption: (['Correlation threshold'], ['Significance threshold'])
lfcdCorrelationThreshold: (0.6, 0.001)
memoryAllocatedForDegreeCentrality: (1.0, 3.0)
run_smoothing: ([1], [0])
runZScoring: ([1], [0])

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

[x] Node timing information:

sorted_node_times.txt

FCP-INDI / cpac_run_logs

app-C-PAC-brainlife.io v0.0.0.dev / C-PAC v1.7.2 - fmriprep-options #8

C-PAC Run Info