aslprep.interfaces.utility module
Utility interfaces for ASLPrep.
- class CombineMotionParameters(from_file=None, resource_monitor=None, **inputs)[source]
Bases:
SimpleInterface
Combine motion parameter files from MCFLIRT across image types.
- Optional Inputs:
aslcontext (a pathlike object or string representing an existing file)
mat_files (a list of items which are a list of items which are a pathlike object or string representing an existing file)
par_files (a list of items which are a pathlike object or string representing an existing file)
volume_types (a list of items which are a string)
- Outputs:
combined_par_file (a pathlike object or string representing an existing file)
mat_file_list (a list of items which are a pathlike object or string representing an existing file)
- class PairwiseRMSDiff(from_file=None, resource_monitor=None, **inputs)[source]
Bases:
SimpleInterface
Run rmsdiff on each contiguous pair of transform files to build a txt file of rmsd values.
This interface uses
RMSDiff
internally, which may not be a proper nipype pattern.- Mandatory Inputs:
in_files (a list of items which are a pathlike object or string representing an existing file) – Matrix files to compare with each other.
ref_file (a pathlike object or string representing an existing file) – Reference volume.
- Outputs:
out_file (a pathlike object or string representing an existing file) – Output txt file.
- class RMSDiff(**inputs)[source]
Bases:
FSLCommand
Wrapped executable:
rmsdiff
.Run rmsdiff.
- Mandatory Inputs:
matrixfile1 (a pathlike object or string representing an existing file) – First matrix file. Maps to a command-line argument:
%s
(position: 0).matrixfile2 (a pathlike object or string representing an existing file) – Second matrix file. Maps to a command-line argument:
%s
(position: 1).ref_vol (a pathlike object or string representing an existing file) – Reference volume. Maps to a command-line argument:
%s
(position: 2).
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.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:
{}
)output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
- Outputs:
rmsd (a float)
- class ReduceASLFiles(from_file=None, resource_monitor=None, **inputs)[source]
Bases:
SimpleInterface
Split ASL data into different files.
- Mandatory Inputs:
asl_file (a pathlike object or string representing an existing file) – ASL file to split.
aslcontext (a pathlike object or string representing an existing file) – Aslcontext TSV.
- Optional Inputs:
metadata (a dictionary with keys which are any value and with values which are any value)
processing_target (a string)
- Outputs:
asl_file (a pathlike object or string representing an existing file) – Modified ASL file.
aslcontext (a pathlike object or string representing an existing file) – Modified aslcontext file.
metadata (a dictionary with keys which are any value and with values which are any value)
- class Smooth(check_import=True, *args, **kwargs)[source]
Bases:
NilearnBaseInterface
,SimpleInterface
Smooth image.
- Mandatory Inputs:
in_file (a pathlike object or string representing an existing file) – An image to smooth.
- Optional Inputs:
fwhm (a float or a list of from 3 to 3 items which are a float) – Full width at half maximum. Smoothing strength, as a full-width at half maximum, in millimeters.
out_file (a pathlike object or string representing a file) – The name of the smoothed file to write out. smooth_img.nii.gz by default. (Nipype default value:
smooth_img.nii.gz
)
- Outputs:
out_file (a pathlike object or string representing an existing file) – Smoothed output file.
- class SplitByVolumeType(from_file=None, resource_monitor=None, **inputs)[source]
Bases:
SimpleInterface
Split out a specific volume type from the ASL file.
- Optional Inputs:
asl_file (a pathlike object or string representing an existing file)
aslcontext (a pathlike object or string representing an existing file)
- Outputs:
out_files (a list of items which are a pathlike object or string representing an existing file)
volume_types (a list of items which are a string)