caps.functional_connectivity.spatial_preproc.SpatialPreproc

SpatialPreproc

class caps.functional_connectivity.spatial_preproc.SpatialPreproc

Spatial fMRI preproc with CONN (realignment/slicetiming/ ” “coregistration/segmentation/normalization/smoothing) and initialization” “of conn_* project

Inputs

[Mandatory]

anatomical_paths: a legal value (mandatory) paths to all subjects anatomical directories

functional_paths: a legal value (mandatory) paths to all subjects functional directories

raw_anatomical_images: a legal value (mandatory) the anatomical files to spatially preprocess

raw_anatomical_prefix: a string (mandatory) the prefix of the raw anatomical images

raw_functional_images: a legal value (mandatory) the functional files to spatially preprocess

raw_functional_prefixes: a legal value (mandatory) the prefixes of the raw functional imagesassociated to the sessions to include

steps: a legal value (mandatory) spatial preprocessing steps. Default to all steps: [‘segmentation’,’slicetiming’, ‘realignment’,’coregistration’,’normalization’, ‘smoothing’]

t_r: a float (mandatory) Repetition time (seconds) [2]

[Optional]

nessions: an integer (optional) Number of sessions

nsubjects: an integer (optional) Number of subjects

slice_order: any value (optional) (option for slicetiming step) acquisition order (vector of indexes; 1=first slice in image)

smoothing_fwhm: an integer (optional) Smoothing factor (mm) [8]

template_functional: a file name (optional) functional template file for normalization [spm/template/EPI.nii]

template_structural: a file name (optional) anatomical template file for approximate coregistration [spm/template/T1.nii]

voxel_size: an integer (optional) target voxel size (mm) [2]

Outputs

CSF_masks: a legal value the spatially preprocessed CSF masks, output ofsegmentation step

Grey_masks: a legal value the spatially preprocessed Grey masks, output ofsegmentation step

White_masks: a legal value the spatially preprocessed White masks, output ofsegmentation step

conn_batch: a legal value the generated conn batch

normalized: an integer 1/0 are the spatially preprocessed images normalized or not

realignment_covariate_files: a legal value the realignment parameters files output ofrealignment step

realignment_covariate_name: a legal value name of the realignment covariate

single_condition_duration: a legal value duration inf for the single condition

single_condition_name: a legal value one single condition named ‘Session’ set to model the entire session data

single_condition_onset: a legal value onset 0.0 for the single condition

spreproc_anatomical_images: a legal value spatially preprocessed anatomical images

spreproc_functional_images: a legal value spatially preprocessed functionale images