t2smap_workflow(data, tes, out_dir='.', mask=None, prefix='', convention='bids', fittype='loglin', fitmode='all', combmode='t2s', debug=False, quiet=False)[source]

Estimate T2 and S0, and optimally combine data across TEs.

  • data (str or list of str) – Either a single z-concatenated file (single-entry list or str) or a list of echo-specific files, in ascending order.

  • tes (list) – List of echo times associated with data in milliseconds.

  • out_dir (str, optional) – Output directory.

  • mask (str, optional) – Binary mask of voxels to include in TE Dependent ANAlysis. Must be spatially aligned with data.

  • fittype ({‘loglin’, ‘curvefit’}, optional) – Monoexponential fitting method. ‘loglin’ means to use the the default linear fit to the log of the data. ‘curvefit’ means to use a monoexponential fit to the raw data, which is slightly slower but may be more accurate.

  • fitmode ({‘all’, ‘ts’}, optional) – Monoexponential model fitting scheme. ‘all’ means that the model is fit, per voxel, across all timepoints. ‘ts’ means that the model is fit, per voxel and per timepoint. Default is ‘all’.

  • combmode ({‘t2s’, ‘paid’}, optional) – Combination scheme for TEs: ‘t2s’ (Posse 1999, default), ‘paid’ (Poser).

Other Parameters
  • debug (bool, optional) – Whether to run in debugging mode or not. Default is False.

  • quiet (bool, optional) – If True, suppress logging/printing of messages. Default is False.


This workflow writes out several files, which are described below:




Limited estimated T2* 3D map or 4D timeseries. Will be a 3D map if fitmode is ‘all’ and a 4D timeseries if it is ‘ts’.


Limited S0 3D map or 4D timeseries.


Full T2* map/timeseries. The difference between the limited and full maps is that, for voxels affected by dropout where only one echo contains good data, the full map uses the single echo’s value while the limited map has a NaN.


Full S0 map/timeseries.


Optimally combined timeseries.