happy2std

Description:

This is a utility for registering happy output maps to standard coordinates. NB: this will only work if you have a working FSL installation.

Inputs:

inputfileroot - the root name of the input NIFTI files (up and including the ‘desc’ but not the underscore).

outputdir - The location for the output files

featdirectory - Either a feat-like directory (x.feat or x.ica) or an fmriprep derivativesanat directory where the information needed for registration to standard space can be found

Outputs:

The happy maps, transformed to MNI152 space

Usage:

Register happy output maps to standard space.

usage: happy2std inputfileroot outputdir featdirectory

Positional Arguments

inputfileroot

the root name of the input NIFTI files (up and including the ‘desc’ but not the underscore).

outputdir

The location for the output files

featdirectory

Either a feat-like directory (x.feat or x.ica) or an fmriprep derivativesanat directory where the information needed for registration to standard space can be found

Named Arguments

--all

Also transform the corrout file (warning - file may be huge).

Default: False

--hires

Transform to match the high resolution anatomic image rather than the standard.

Default: False

--linear

Only do linear transformation, even if warpfile exists.

Default: False

--onefile

Align a single file, specified by name without extension (ignore INPUTFILEROOT).

--fake

Output, but do not execute, alignment commands.

Default: False