Developers - API

Workflows

post processing the bold

xcp_d.workflow.bold.init_boldpostprocess_wf(lower_bpf, upper_bpf, bpf_order, motion_filter_order, motion_filter_type, bandpass_filter, band_stop_min, band_stop_max, smoothing, bold_file, head_radius, params, custom_conf, omp_nthreads, dummytime, output_dir, fd_thresh, num_bold, mni_to_t1w, despike, brain_template='MNI152NLin2009cAsym', layout=None, name='bold_postprocess_wf')[source]

This workflow organizes bold processing workflow.

Workflow Graph

(Source code)

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

contigvol: int

number of contigious volumes

despike: bool

afni depsike

motion_filter_order: int

respiratory motion filter order

motion_filter_type: str

respiratory motion filter type: lp or notch

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_conf: str

path to cusrtom nuissance regressors

dummytime: float

the first vols 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

(Source code)

post processing the bold

xcp_d.workflow.cifti.init_ciftipostprocess_wf(cifti_file, lower_bpf, upper_bpf, bpf_order, motion_filter_order, motion_filter_type, bandpass_filter, band_stop_min, band_stop_max, smoothing, head_radius, params, output_dir, custom_conf, omp_nthreads, dummytime, fd_thresh, mni_to_t1w, despike, num_cifti, layout=None, name='cifti_process_wf')[source]

This workflow organizes 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

contigvol: int

number of contigious volumes

despike: bool

afni depsike

motion_filter_order: int

respiratory motion filter order

motion_filter_type: str

respiratory motion filter type: lp or notch

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_conf: str

path to cusrtom nuissance regressors

scrub: bool

remove the censored volumes

dummytime: float

the first vols in 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