simdata

Description:

Generates a simulated rapidtide dataset.

Inputs:

Outputs:

Usage:

Generate simulated fMRI data with known correlation parameters

usage: simdata [-h] [--lfopctfile FILE] [--lfolagfile FILE]
               [--lforegressor FILE] [--lfosamprate SAMPRATE]
               [--lfostarttime STARTTIME] [--resppctfile FILE]
               [--resplagfile FILE] [--respregressor FILE]
               [--respsamprate SAMPRATE] [--respstarttime STARTTIME]
               [--cardiacpctfile FILE] [--cardiaclagfile FILE]
               [--cardiacregressor FILE] [--cardiacsamprate SAMPRATE]
               [--cardiacstarttime STARTTIME] [--numskip SKIP]
               [--globalnoiselevel LEVEL] [--voxelnoiselevel LEVEL] [--debug]
               fmrifilename immeanfilename outputroot slicetimefile

Positional Arguments

fmrifilename

Input NIFTI file name. An exemplar BOLD fMRI file with the target dimensions

immeanfilename

Input NIFTI file name. 3D file with the mean value for each voxel

outputroot

Root name for the output files.

slicetimefile

Slice acquisition time file, either FSL format or BIDS sidecar.

Named Arguments

--lfopctfile

3D NIFTI file with the lfo amplitude in percent of mean at every point

--lfolagfile

3D NIFTI file with the lfo delay value in seconds at every point

--lforegressor

The LFO regressor text file

--lfosamprate

The sample rate of the LFO regressor file, in Hz

--lfostarttime

The time delay, in seconds, into the lfo regressor file that matches the start time of the fmrifile. Default is 0.0

--resppctfile

3D NIFTI file with the resp amplitude in percent of mean at every point

--resplagfile

3D NIFTI file with the resp delay value in seconds at every point

--respregressor

The LFO regressor text file

--respsamprate

The sample rate of the LFO regressor file, in Hz

--respstarttime

The time delay, in seconds, into the resp regressor file that matches the start time of the fmrifile. Default is 0.0

--cardiacpctfile

3D NIFTI file with the cardiac amplitude in percent of mean at every point

--cardiaclagfile

3D NIFTI file with the cardiac delay value in seconds at every point

--cardiacregressor

The LFO regressor text file

--cardiacsamprate

The sample rate of the LFO regressor file, in Hz

--cardiacstarttime

The time delay, in seconds, into the cardiac regressor file that matches the start time of the fmrifile. Default is 0.0

--numskip

Use to simulate tr periods deleted during preprocessing

Default: 0

--globalnoiselevel

The variance of the noise common to every voxel. Default is 0.0

Default: 0.0

--voxelnoiselevel

The variance of the voxel specific noise. Default is 0.0

Default: 0.0

--debug

Enable additional debugging output.

Default: False