caps.functional_preproc.pypreprocess_fmri_preproc.SubjectPreprocessing¶
SubjectPreprocessing¶
- class caps.functional_preproc.pypreprocess_fmri_preproc.SubjectPreprocessing(autoexport_nodes_parameters=True, **kwargs)[source]¶
Preprocessing fMRI data for a single subject.
Inputs¶
[Mandatory]
anat_file: a file name (mandatory)
Path to the anatomical image
|
func_file: a file name or a legal value or an implementor of, or
can be adapted to implement, _Undefined or None (mandatory)
Path to the functional image(s)
|
fwhm: a legal value or a float or an implementor of, or can be
adapted to implement, _Undefined or None (mandatory)
FWHM for smoothing the functional data. If normalize is set, then
this parameter is based to spm.Normalize, else spm.Smooth is used
to explicitly smooth the functional data.
|
repetition_time: a float (mandatory)
The repetition time of the functional iamge acquisition sequence.
|
slice_order: a legal value (mandatory)
The acquistion order of each slice of the functional iamge.
|
[Optional]
coreg_anat_to_func: a boolean (optional)
If set, then functional data will be the reference during
coregistration. By default the anatomical data if the reference,
to ensure a precise registration (since anatomical data has finer
resolution)
|
coregister: a boolean (optional)
If set, the functional and anatomical images will be
corregistered. If this not set, and anatomical image is defined,
it is assumed that functional and anatomical images have already
been coregistered.
|
normalize: a boolean (optional)
If set, then the subject_data (functional and anatomical) will be
warped into MNI space
|
realign: a boolean (optional)
If set, then the functional data will be realigned to correct for
head-motion.
|
segment: a boolean (optional)
If set, then the subject’s anatomical image will be segmented to
produce GM, WM, and CSF compartments (useful for both indirect
normalization (intra-subject) or DARTEL (inter-subject) alike
|
slice_time: a boolean (optional)
If set, then the functional data will be correction for slice
timing distortions.
|
Outputs¶
coregister_file: a file name or a legal value or an implementor
of, or can be adapted to implement, _Undefined or None
The coregister image(s).
|
mean_file: a file name or a legal value or an implementor of, or
can be adapted to implement, _Undefined or None
The functional realigned mean image.
|
normalize_anat_file: a file name or a legal value or an
implementor of, or can be adapted to implement, _Undefined or None
The normalize file(s)
|
normalize_func_file: a file name or a legal value or an
implementor of, or can be adapted to implement, _Undefined or None
The normalize file(s)
|
realign_file: a file name or a legal value or an implementor of,
or can be adapted to implement, _Undefined or None
The functional realigned image(s) (head-motion correction).
|
segment_file: a file name or a legal value or an implementor of,
or can be adapted to implement, _Undefined or None
|
slice_time_corrected_file: a file name or a legal value or an
implementor of, or can be adapted to implement, _Undefined or None
The functional slice time corrected image(s).
|
smooth_normalize_func_file: a file name or a legal value or an
implementor of, or can be adapted to implement, _Undefined or None
The normalize and smoothed functional file(s)
|
transformation_file: a file name or a legal value or an
implementor of, or can be adapted to implement, _Undefined or None
The functional realigned transformation parameters.
|
Pipeline schema¶
