Specify Processing Steps in Design File

The processing steps to perform in the analysis of the image data can be predefined in the design file. This is done by selecting the processing steps that should be performed and altering them, if necessary, to match the steps you would like to perform in the analysis.

Process

Specify the processing steps to be performed in the analysis.

Preprocessing

Check to perform preprocessing.

GLM

Check to estimate GLM. Note that the statistical analysis is performed automatically by the program.

Preprocessing Steps

Specify the preprocessing steps to perform prior to estimation of the GLM and the statistical analysis. This is done by selecting the preocessing steps that should be performed and altering them, if necessary, to match the steps you would like to perform in the analysis.

Slice Time Correction

Check to perform slice time correction. Please note that it is the users 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 block designs, slice time correction might not be critical

Specify 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.

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 millimeters of the filter can also be altered. By default, the FWHM is about twice the voxel size in all directions.

High-Pass Filtering

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.

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.

Other Options

Cancel Button

Abort edit of existing, or creation of new, design file.

Save Design Button

Save design file with the name specified in design name.

Previous Button

Go to the previous page.