aslprep.interfaces.multiecho module

Interfaces for working with multi-echo data.

class T2SMap(command=None, terminal_output=None, write_cmdline=False, **inputs)[source]

Bases: CommandLine

Wrapped executable: t2smap.

Run the tedana T2* workflow to generate a T2* map and create a combined time series.

Example

>>> from fmriprep.interfaces import multiecho
>>> t2smap = multiecho.T2SMap()
>>> t2smap.inputs.in_files = ['sub-01_run-01_echo-1_bold.nii.gz',                                   'sub-01_run-01_echo-2_bold.nii.gz',                                   'sub-01_run-01_echo-3_bold.nii.gz']
>>> t2smap.inputs.echo_times = [0.013, 0.027, 0.043]
>>> t2smap.cmdline  
't2smap -d sub-01_run-01_echo-1_bold.nii.gz sub-01_run-01_echo-2_bold.nii.gz sub-01_run-01_echo-3_bold.nii.gz -e 13.0 27.0 43.0 --fittype curvefit'
Mandatory Inputs:

  • echo_times (a list of at least 3 items which are a float) – Echo times. Maps to a command-line argument: -e %s (position: 2).

  • in_files (a list of at least 3 items which are a pathlike object or string representing an existing file) – Multi-echo BOLD EPIs. Maps to a command-line argument: -d %s (position: 1).

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: {})

  • fittype (‘curvefit’ or ‘loglin’) – Desired fitting method: “loglin” means that a linear model is fit to the log of the data. “curvefit” means that a more computationally demanding monoexponential model is fit to the raw data. Maps to a command-line argument: --fittype %s (position: 3). (Nipype default value: curvefit)

Outputs:

  • optimal_comb (a pathlike object or string representing an existing file) – Optimally combined ME-EPI time series.

  • s0_map (a pathlike object or string representing an existing file) – Limited S0 map.

  • t2star_map (a pathlike object or string representing an existing file) – Limited T2* map.