Developers - API
Workflows
Workflows for post-processing the BOLD data.
post processing the bold
- xcp_d.workflow.bold.init_boldpostprocess_wf(lower_bpf, upper_bpf, bpf_order, motion_filter_type, motion_filter_order, bandpass_filter, band_stop_min, band_stop_max, smoothing, bold_file, head_radius, params, custom_confounds, omp_nthreads, dummytime, output_dir, fd_thresh, num_bold, mni_to_t1w, despike, layout=None, name='bold_postprocess_wf')[source]
Organize the bold processing workflow.
- Workflow Graph
- bold_file: str
bold file for post processing
- lower_bpffloat
Lower band pass filter
- upper_bpffloat
Upper band pass filter
- layoutBIDSLayout object
BIDS dataset layout
- despike: bool
If True, run 3dDespike from AFNI
- motion_filter_type: str
respiratory motion filter type: lp or notch
- motion_filter_order: int
order for motion filter
- band_stop_min: float
respiratory minimum frequency in breathe per minutes(bpm)
- band_stop_max,: float
respiratory maximum frequency in breathe per minutes(bpm)
- layoutBIDSLayout object
BIDS dataset layout
- omp_nthreadsint
Maximum number of threads an individual process may use
- output_dirstr
Directory in which to save xcp_d output
- fd_thresh
Criterion for flagging framewise displacement outliers
- head_radiusfloat
radius of the head for FD computation
- params: str
nuissance regressors to be selected from fmriprep regressors
- smoothing: float
smooth the derivatives output with kernel size (fwhm)
- custom_confounds: str
path to cusrtom nuissance regressors
- dummytime: float
the time in seconds to be removed before postprocessing
- bold_file
BOLD series NIfTI file
- mni_to_t1w
MNI to T1W ants Transformation file/h5
- ref_file
Bold reference file from fmriprep
- bold_mask
bold_mask from fmriprep
- cutstom_conf
custom regressors
- processed_bold
clean bold after regression and filtering
- smoothed_bold
smoothed clean bold
- alff_out
alff niifti
- smoothed_alff
smoothed alff
- reho_out
reho output computed by afni.3dreho
- sc217_ts
schaefer 200 timeseries
- sc217_fc
schaefer 200 func matrices
- sc417_ts
schaefer 400 timeseries
- sc417_fc
schaefer 400 func matrices
- gs360_ts
glasser 360 timeseries
- gs360_fc
glasser 360 func matrices
- gd333_ts
gordon 333 timeseries
- gd333_fc
gordon 333 func matrices
- qc_file
quality control files
Workflows for post-processing CIFTI-format BOLD data.
post processing the bold
- xcp_d.workflow.cifti.init_ciftipostprocess_wf(cifti_file, lower_bpf, upper_bpf, bpf_order, motion_filter_type, motion_filter_order, bandpass_filter, band_stop_min, band_stop_max, smoothing, head_radius, params, output_dir, custom_confounds, omp_nthreads, dummytime, fd_thresh, mni_to_t1w, despike, num_cifti, layout=None, name='cifti_process_wf')[source]
Organize the cifti processing workflow.
- Workflow Graph
- bold_file: str
bold file for post processing
- lower_bpffloat
Lower band pass filter
- upper_bpffloat
Upper band pass filter
- layoutBIDSLayout object
BIDS dataset layout
- despike: bool
afni depsike
- motion_filter_type: str
respiratory motion filter type: lp or notch
- motion_filter_order: int
order for motion filter
- band_stop_min: float
respiratory minimum frequency in breathe per minutes(bpm)
- band_stop_max,: float
respiratory maximum frequency in breathe per minutes(bpm)
- layoutBIDSLayout object
BIDS dataset layout
- omp_nthreadsint
Maximum number of threads an individual process may use
- output_dirstr
Directory in which to save xcp_d output
- fd_thresh
Criterion for flagging framewise displacement outliers
- head_radiusfloat
radius of the head for FD computation
- params: str
nuissance regressors to be selected from fmriprep regressors
- smoothing: float
smooth the derivatives output with kernel size (fwhm)
- custom_confounds: str
path to cusrtom nuissance regressors
- scrub: bool
remove the censored volumes
- dummytime: float
the first few seconds to be removed before postprocessing
- cifti_file
CIFTI file
- cutstom_conf
custom regressors
- processed_bold
clean bold after regression and filtering
- smoothed_bold
smoothed clean bold
- alff_out
alff niifti
- smoothed_alff
smoothed alff
- reho_lh
reho left hemisphere
- reho_rh
reho right hemisphere
- sc217_ts
schaefer 200 timeseries
- sc217_fc
schaefer 200 func matrices
- sc417_ts
schaefer 400 timeseries
- sc417_fc
schaefer 400 func matrices
- gs360_ts
glasser 360 timeseries
- gs360_fc
glasser 360 func matrices
- gd333_ts
gordon 333 timeseries
- gd333_fc
gordon 333 func matrices
- qc_file
quality control files