rapidtide2std

Description:

This is a utility for registering rapidtide output maps to standard coordinates. It’s usually much faster to run rapidtide in native space then transform afterwards to MNI152 space. NB: this will only work if you have a working FSL installation.

Inputs:

Outputs:

New versions of the rapidtide output maps, registered to either MNI152 space or to the hires anatomic images for the subject. All maps are named with the specified root name with ‘_std’ appended.

Usage:

Register rapidtide output maps to standard space.

usage: rapidtide2std [-h] [--all] [--hires] [--linear] [--onefile FILE]
                     [--sequential] [--fake] [--debug]
                     inputfileroot outputdir featdirectory

Positional Arguments

inputfileroot

the root name of the input NIFTI files (up to but not including the underscore).

outputdir

The location for the output files

featdirectory

Either a feat directory (x.feat) or an fmriprep derivatives anat 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).

--sequential

Execute commands sequentially - do not submit to the cluster.

Default: False

--fake

Output, but do not execute, alignment commands.

Default: False

--debug

Output additional debugging information.

Default: False