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mvpa.misc.fsl.base

Tiny snippets to interface with FSL easily.

The comprehensive API documentation for this module, including all technical details, is available in the Epydoc-generated API reference for mvpa.misc.fsl.base (for developers).

Classes

FslEV3

class mvpa.misc.fsl.base.FslEV3(source)

Bases: mvpa.misc.io.base.ColumnData

IO helper to read FSL’s EV3 files.

This is a three-column textfile format that is used to specify stimulation protocols for fMRI data analysis in FSL’s FEAT module.

Data is always read as float.

Read and write FSL EV3 files.

Parameters:
  • source (filename of an EV3 file) –
durations
durations
getEV(evid)
Returns a tuple of (onset time, simulus duration, intensity) for a certain EV.
getNEVs()
Returns the number of EVs in the file.
intensities
intensities
nevs
Returns the number of EVs in the file.
onsets
onsets
toEvents()
Convert into a list of Event instances.
tofile(filename)
Write data to a FSL EV3 file.

See also

Derived classes might provide additional methods via their base classes. Please refer to the list of base classes (if it exists) at the begining of the FslEV3 documentation.

Full API documentation of FslEV3 in module mvpa.misc.fsl.base.

McFlirtParams

class mvpa.misc.fsl.base.McFlirtParams(source)

Bases: mvpa.misc.io.base.ColumnData

Read and write McFlirt’s motion estimation parameters from and to text files.

Parameters:
  • source (str) – Filename of a parameter file.
plot()

Produce a simple plot of the estimated translation and rotation parameters using.

You still need to can pylab.show() or pylab.savefig() if you want to see/get anything.

toarray()
Returns the data as an array with six columns (same order as in file).
tofile(filename)
Write motion parameters to file.

See also

Derived classes might provide additional methods via their base classes. Please refer to the list of base classes (if it exists) at the begining of the McFlirtParams documentation.

Full API documentation of McFlirtParams in module mvpa.misc.fsl.base.