simdata

Description:

Generates a simulated rapidtide dataset.

Inputs:

Outputs:

Usage:

Generate simulated fMRI data with known correlation parameters

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

Positional Arguments

fmritr

TR of the simulated data, in seconds.

numtrs

Number of TRs in the simulated data.

immeanfilename

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

outputroot

Root name for the output files.

Named Arguments

--slicetimefile

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

--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, as percent of the voxel mean. Default is 0.0

Default: 0.0

--debug

Enable additional debugging output.

Default: False

LFO band options

--lfopctfile

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

--lfosignalfraction

3D NIFTI file with the lfo amplitude expressed as the percentage of inband variance accounted for by the regressor

--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

Resp band options

--resppctfile

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

--respsignalfraction

3D NIFTI file with the resp amplitude expressed as the percentage of inband variance accounted for by the regressor

--resplagfile

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

--respregressor

The resp regressor text file

--respsamprate

The sample rate of the resp 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

Cardiac band options

--cardiacpctfile

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

--cardiacsignalfraction

3D NIFTI file with the cardiac amplitude expressed as the percentage of inband variance accounted for by the regressor

--cardiaclagfile

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

--cardiacregressor

The cardiac regressor text file

--cardiacsamprate

The sample rate of the cardiac 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