eXtensible Connectivity Pipeline-style quality control files¶

Generate eXtensible Connectivity Pipeline-style quality control files

Columns¶

substr: subject label [1]
sesstr: session label [1]
taskstr: task label [1]
runint: run index [1]
descstr: description [1]
regressorsstr: ‘Name’ of regressors in the current fork
spacestr: space label [1]
meanFDfloat: mean Jenkinson framewise displacement [2] CPAC.generate_motion_statistics.calculate_FD_J after preprocessing
relMeansRMSMotionfloat: “mean value of RMS motion” [3]
relMaxRMSMotionfloat: “maximum vaue of RMS motion” [3]
meanDVInitfloat: “mean DVARS” [3]
meanDVFinalfloat: “mean DVARS” [3]
nVolCensoredint: “total number of volume(s) censored [3]
nVolsRemovedint: number of volumes in derivative minus number of volumes in original functional scan
motionDVCorrInitfloat: “correlation of RMS and DVARS before regresion” [3]
motionDVCorrFinalfloat: “correlation of RMS and DVARS after regresion” [3]
coregDicefloat: “Coregsitration of Functional and T1w:[…] Dice index” [3]
coregJaccardfloat: “Coregsitration of Functional and T1w:[…] Jaccard index” [3]
coregCrossCorrfloat: “Coregsitration of Functional and T1w:[…] cross correlation” [3]
coregCoveragfloat: “Coregsitration of Functional and T1w:[…] Coverage index” [3]
normDicefloat: “Normalization of T1w/Functional to Template:[…] Dice index” [3]
normJaccardfloat: “Normalization of T1w/Functional to Template:[…] Jaccard index” [3]
normCrossCorrfloat: “Normalization of T1w/Functional to Template:[…] cross correlation” [3]
normCoveragefloat: “Normalization of T1w/Functional to Template:[…] Coverage index” [3]

CPAC.qc.xcp.dvcorr(dvars, fdj)[source]¶: Function to correlate DVARS and FD-J

CPAC.qc.xcp.generate_xcp_qc(sub, ses, task, run, desc, regressors, bold2t1w_mask, t1w_mask, bold2template_mask, template_mask, original_func, final_func, movement_parameters, dvars, censor_indices, framewise_displacement_jenkinson, dvars_after, template)[source]¶

Function to generate an RBC-style QC CSV

Parameters

substr: subject ID
sesstr: session ID
taskstr: task ID
runstr or int: run ID
descstr: description string
regressorsstr: ‘Name’ of regressors in fork
original_funcstr: path to original ‘bold’ image
final_boldstr: path to ‘space-template_desc-preproc_bold’ image
bold2t1w_maskstr: path to bold-to-T1w transform applied to space-bold_desc-brain_mask with space-T1w_desc-brain_mask reference
t1w_maskstr: path to space-T1w_desc-brain_mask
bold2template_maskstr: path to space-template_desc-bold_mask
template_maskstr: path to space-template_desc-T1w_mask
movement_parameters: str: path to movement parameters
dvarsstr: path to DVARS before motion correction
censor_indiceslist: list of indices of censored volumes
framewise_displacement_jenkinsonstr: path to framewise displacement (Jenkinson) before motion correction
dvars_afterstr: path to DVARS on final ‘bold’ image
templatestr: path to registration template

Returns

str: path to space-template_desc-xcp_quality TSV

CPAC.qc.xcp.get_bids_info(subject, scan, wf_name)[source]¶

Function to gather BIDS information from a strat_pool

Parameters

subjectstr: subject ID
scanstr: scan ID
wf_namestr: workflow name

Returns

subjectstr: subject ID
sessionstr: session ID
taskstr: task ID
runstr or int: run ID

Examples

>>> subject, session, task, run = get_bids_info(
...     subject='DavidBowman', scan='rest_acq-1_run-1',
...     wf_name='cpac_DavidBowman_3')
>>> subject
'DavidBowman'
>>> session
'3'
>>> task
'rest'
>>> run
'1'
>>> get_bids_info(subject='sub-colornest035', scan='rest_run-01',
...               wf_name='cpac_sub-colornest035_ses-1')
('colornest035', '1', 'rest', '1')

CPAC.qc.xcp.qc_xcp(wf, cfg, strat_pool, pipe_num, opt=None)[source]¶

{‘name’: ‘qc_xcp’,

‘config’: [‘pipeline_setup’, ‘output_directory’, ‘quality_control’], ‘switch’: [‘generate_xcpqc_files’], ‘option_key’: ‘None’, ‘option_val’: ‘None’, ‘inputs’: [(‘subject’, ‘scan’, ‘bold’, ‘desc-preproc_bold’,

‘space-T1w_desc-mean_bold’, ‘space-T1w_desc-brain_mask’, ‘max-displacement’, ‘space-template_desc-preproc_bold’, ‘space-bold_desc-brain_mask’, [‘T1w-brain-template-mask’, ‘EPI-template-mask’], [‘space-template_desc-bold_mask’, ‘space-EPItemplate_desc-bold_mask’], ‘regressors’, [‘T1w-brain-template-funcreg’, ‘EPI-brain-template-funcreg’], ‘movement-parameters’, ‘dvars’, ‘framewise-displacement-jenkinson’)],

‘outputs’: [‘space-template_desc-xcp_quality’]}

References

1: BIDS-contributors. 2021. Appendix IX: Entities. The Brain Imaging Data Structure (BIDS) Specification, 1.6.0
2: Jenkinson, M., Bannister, P., Brady, M., and Smith, S. 2002 October. Improved optimization for the robust and accurate linear registration and motion correction of brain images. Neuroimage, 17 :2 , pp. 825–841 doi:10.1006/nimg.2002.1132
3: Ciric, R., Rosen, A. F. G., Erus, G., Cieslak, M., Adebimpe, A., Cook, P. A., Bassett, D. S., Davatzikos, C., Wolf, D. H., and Satterthwaite, T. D. 2019. Quality control dictionary. xcpEngine 1.0 documentation, a7254873