Advanced Settings

The advanced settings, contains three tabs:

Design Tab which holds information about the design matrix. Here the hemodynamic response function (HRF) can be modified as well.
Preprocessing Tab where preprocessing steps can be modified, and/or turned on/off.
GLM Settings Tab where settings used in the GLM estimation can be modified.

Design Tab

Design Matrix button

Displays the design matrix.

The design matrix models the input paradigm, where the stimulus is convolved with a HRF. It is used in the GLM estimation.

Design Graph button

Design Graphs

Displays the design matrix graphically.

Boxcar Graphs

Displays the input paradigm as a boxcar graph.

Edit HRF button

Permits editing of the Hemodynamic Response Function (HRF) used to convolve the input paradigm read from the design file to generate the design matrix.

Preprocessing Tab

Specify the preprocessing steps that should be performed prior to the GLM estimation and the statistical analysis.

Slice Time Correction

Check to perform slice time correction. Please note that it is the user’s responsibility to set up the slice time acquisition mode.

Slice time correction is done to correct for the fact that for a given volume in the image time-series, each slice is acquired at a different time point. The correction is done using spline interpolation. For blocked designs, slice time correction might not be critical

Specifying Slice Time Acquisition Mode

Specifying the slice time acquisition mode is the same as setting up the order of the acquisition. The different possibilities are:

· Interleaved ascending (odd start scan)

· Interleaved descending (odd start scan)

· Interleaved ascending (even start scan)

· Interleaved descending (even start scan)

· Sequential ascending

· Sequential descending

Note that the slices are numbered from 1. Therefore, if there are 10 slices in a volume, an ascending interleaved sequence with odd start scan would be {1-3-5-7-9-2-4-6-8-10}.

Motion Correction

Check to perform motion correction.

Motion correction is done to correct for subject movement in the scanner, by estimating the rotation and translation of the volumes in the image time series to a reference volume. Then the volumes are shifted according to the estimated rotation and translation, using a cubic shift operation.

Motion Graph button

Display the estimated rotation and translation parameters graphically. Choose which parameters to display from the drop down menu as illustrated below. The button is enabled after motion correction has been performed.

Rotation Graphs

Display estimated rotation parameters graphically.

Translation Graphs

Displays estimated translation parameters graphically.

Gaussian Smoothing (Spatial)

Check to perform Gaussian spatial smoothing.

Gaussian spatial smoothing is performed to blur and reduce high-frequency spatial noise in the images. The user can alter the dimensionality of the filter, applying either a two-dimensional (within slice) or a three-dimensional (within volume) filter. The full-width-half-maximum (FWHM) in millimetres of the filter can also be altered. By default, the FWHM is about twice the voxel size in all directions.

High-Pass Filter

Check to perform temporal high-pass filtering.

A temporal high-pass filter is applied to reduce low frequency drifts in the image time series. In this application a Butterworth filter is applied. The user can choose to either specify the filter's wavelength in seconds or the cutoff frequency in Hz. Specifying a wavelength of e.g. 120 seconds as below, results in a cutoff frequency of 1/120 Hz. This means that frequencies below the cutoff frequency are filtered out of the image time series. Therefore, it can be dangerous to apply this filter if the right wavelength/cutoff frequency is not specified. The frequencies that are filtered out are illustrated graphically by pressing the view design in frequency button.

Please note that using a wavelength in seconds that is too short for the given problem, you might end up filtering out the BOLD response. It is the user's responsibility to set up the correct wavelength.

Wavelength in Seconds

Specify the wavelength of the high-pass filter in seconds. The cutoff frequency in Hz is automatically updated.

Cutoff Frequency in Hz

Specify the cutoff frequency of the high-pass filter in Hz. The wavelength in seconds is automatically updated.

View Design In Frequency Button

Press to view the design matrix graphically in the frequency domain. The vertical line illustrates the cutoff frequency.

Note that frequencies from 0 to the vertical line are filtered out.

Drop Down Menu

Use drop-down menu to alternate between different regressors in the design matrix.

View All

Check to display all the regressors in design matrix.

GLM Settings Tab

Holds settings related to the GLM estimation which can be changed by the user.

Temporal Smoothing

Temporal smoothing using a Gaussian filter is performed for the GLM estimation. It will influence the degrees of freedom used in the statistical analysis.

Temporal Smoothing On

Check to turn on temporal smoothing. By default, temporal smoothing filter is on. It is applied both to the image data and the design matrix.

FWHM in Seconds

Set the FWHM of the temporal smoothing filter. The default value is 4 seconds.

Threshold Data

Thresholding of the image data is done only for the GLM estimation, so that the image voxel information in the time series will not be affected by the threshold. A default threshold value is estimated automatically when the BOLD module is opened, as the mean intensity of the first volume, divided by 4. The voxels with intensity below the threshold is marked in red. In the GLM estimation, the first volume is used as a reference point where values below the given threshold for this volume, will be omitted in the estimation. The output of the GLM estimation corresponding to these voxels will therefore be zero.

Threshold On

Check to turn on voxel threshold. The default is on.

Display Voxel Threshold

Check to display voxels which are not included in the GLM estimation. The excluded voxels are displayed in red. The default is on.

Threshold Value

Displays voxel threshold value.