smriprep.interfaces.fsl module

class smriprep.interfaces.fsl.FAST(**inputs)[source]

Bases: FAST

Wrapped executable: fast.

A replacement for nipype.interfaces.fsl.preprocess.FAST that allows bias_iters=0 to disable bias field correction entirely

>>> from smriprep.interfaces.fsl import FAST
>>> fast = FAST()
>>> fast.inputs.in_files = 'sub-01_desc-warped_T1w.nii.gz'
>>> fast.inputs.bias_iters = 0
>>> fast.cmdline
'fast -I 0 -S 1 sub-01_desc-warped_T1w.nii.gz'
Mandatory Inputs:

in_files (a list of items which are a pathlike object or string representing an existing file) – Image, or multi-channel set of images, to be segmented. Maps to a command-line argument: %s (position: -1).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • bias_iters (0 <= an integer <= 10) – Number of main-loop iterations during bias-field removal. Maps to a command-line argument: -I %d.

  • bias_lowpass (4 <= an integer <= 40) – Bias field smoothing extent (FWHM) in mm. Maps to a command-line argument: -l %d.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • hyper (0.0 <= a floating point number <= 1.0) – Segmentation spatial smoothness. Maps to a command-line argument: -H %.2f.

  • img_type (1 or 2 or 3) – Int specifying type of image: (1 = T1, 2 = T2, 3 = PD). Maps to a command-line argument: -t %d.

  • init_seg_smooth (0.0001 <= a floating point number <= 0.1) – Initial segmentation spatial smoothness (during bias field estimation). Maps to a command-line argument: -f %.3f.

  • init_transform (a pathlike object or string representing an existing file) – <standard2input.mat> initialise using priors. Maps to a command-line argument: -a %s.

  • iters_afterbias (1 <= an integer <= 20) – Number of main-loop iterations after bias-field removal. Maps to a command-line argument: -O %d.

  • manual_seg (a pathlike object or string representing an existing file) – Filename containing intensities. Maps to a command-line argument: -s %s.

  • mixel_smooth (0.0 <= a floating point number <= 1.0) – Spatial smoothness for mixeltype. Maps to a command-line argument: -R %.2f.

  • no_bias (a boolean) – Do not remove bias field. Maps to a command-line argument: -N.

  • no_pve (a boolean) – Turn off PVE (partial volume estimation). Maps to a command-line argument: --nopve.

  • number_classes (1 <= an integer <= 10) – Number of tissue-type classes. Maps to a command-line argument: -n %d.

  • other_priors (a list of from 3 to 3 items which are a pathlike object or string representing a file) – Alternative prior images. Maps to a command-line argument: -A %s.

  • out_basename (a pathlike object or string representing a file) – Base name of output files. Maps to a command-line argument: -o %s.

  • output_biascorrected (a boolean) – Output restored image (bias-corrected image). Maps to a command-line argument: -B.

  • output_biasfield (a boolean) – Output estimated bias field. Maps to a command-line argument: -b.

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.

  • probability_maps (a boolean) – Outputs individual probability maps. Maps to a command-line argument: -p.

  • segment_iters (1 <= an integer <= 50) – Number of segmentation-initialisation iterations. Maps to a command-line argument: -W %d.

  • segments (a boolean) – Outputs a separate binary image for each tissue type. Maps to a command-line argument: -g.

  • use_priors (a boolean) – Use priors throughout. Maps to a command-line argument: -P.

  • verbose (a boolean) – Switch on diagnostic messages. Maps to a command-line argument: -v.

Outputs:

  • bias_field (a list of items which are a pathlike object or string representing a file)

  • mixeltype (a pathlike object or string representing a file) – Path/name of mixeltype volume file _mixeltype.

  • partial_volume_files (a list of items which are a pathlike object or string representing a file)

  • partial_volume_map (a pathlike object or string representing a file) – Path/name of partial volume file _pveseg.

  • probability_maps (a list of items which are a pathlike object or string representing a file)

  • restored_image (a list of items which are a pathlike object or string representing a file)

  • tissue_class_files (a list of items which are a pathlike object or string representing a file)

  • tissue_class_map (a pathlike object or string representing an existing file) – Path/name of binary segmented volume file one val for each class _seg.