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

sub (str) – subject ID
ses (str) – session ID
task (str) – task ID
run (str or int) – run ID
desc (str) – description string
regressors (str) – ‘Name’ of regressors in fork
original_func (str) – path to original ‘bold’ image
final_bold (str) – path to ‘space-template_desc-preproc_bold’ image
bold2t1w_mask (str) – path to bold-to-T1w transform applied to space-bold_desc-brain_mask with space-T1w_desc-brain_mask reference
t1w_mask (str) – path to space-T1w_desc-brain_mask
bold2template_mask (str) – path to space-template_desc-bold_mask
template_mask (str) – path to space-template_desc-T1w_mask
movement_parameters (str) – path to movement parameters
dvars (str) – path to DVARS before motion correction
censor_indices (list) – list of indices of censored volumes
framewise_displacement_jenkinson (str) – path to framewise displacement (Jenkinson) before motion correction
dvars_after (str) – path to DVARS on final ‘bold’ image
template (str) – path to registration template

Returns

path to space-template_desc-xcp_quality TSV

Return type

str

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

Function to gather BIDS information from a strat_pool

Parameters

subject (str) – subject ID
scan (str) – scan ID
wf_name (str) – workflow name

Returns

subject (str) – subject ID
session (str) – session ID
task (str) – task ID
run (str 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', '01')

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

Node Block:

{'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_sbref', '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': {
                 'Template': 'T1w-brain-template-mask'}}}

References

1(1,2,3,4,5,6): BIDS-contributors. 2022. Appendix IX: Entities. The Brain Imaging Data Structure (BIDS) Specification, 1.7.0
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(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15): 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