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‘/home/ourlab/matlab/fmrlab/ica_linux’). 1.5 Download the FMRLAB example data set
The example data set used in this tutorial can be downloaded from: http://www.sccn.ucsd.edu/fmrlab/example/. This data set contains two files, 2dseq_r1 and 2dseq_str. The first is the file of functional images. The second contains the corresponding structural images. The functional images were acquired during a 5-minute experiment in which the subject was shown brief 8-Hz flickering-checkerboard stimulation lasting 0.5 s every 30 seconds (SOA). (See Duann et al., 2002 for details).
The image acquisition parameters for the functional images were: ????????
Image dimensions = 64 x 64 x 5 FOV = 250 mm x 250 mm Slice thickness = 7 mm TR = 0.5 sec
??Total number of scans = 610 (600 time points) ??Dummy scans = 10
The structural scans were T1-weighted images with the same slice positions, number of slices and FOV as the functional scans. However, they were acquired at 256 x 256 resolution to provide more structural details than the functional scans.
For this data set, the structural image acquisition parameters were: ??????
Image dimensions = 256 x 256 x 5 FOV = 250 mm x 250 mm Slice thickness = 7 mm
2. Functional Image Preprocessing and ICA Decomposition
Next we demonstrate, step-by-step, how to use FMRLAB to analyze the example fMRI data set.
2.1 Start FMRLAB
From the MATLAB command line, type fmrlab. If the environmental variables have been set properly, we recommend starting FMRLAB from the directory where the example image data are located.
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2.2 Quitting FMRLAB
To exit from FMRLAB, select the FMRLAB menu item “Dataset > Quit”. This will clean the workspace, close any figures created by FMRLAB, and clear all the FMRLAB variables, including the FMRLAB global variable structure, FMRI. 2.3 Create an FMRLAB dataset
The procedure for creating an FMRLAB dataset is: (1) Select a functional image file. (2) Enter the image acquisition parameters for the functional scans. (3) Enter the image information for the structural scans. Select Dataset > Create Dataset from the FMRLAB menu. A Select Image File window will pop up (as below) allowing you to select the file containing the functional scans.
Move the mouse cursor to 2dseq_r1 (the functional scan file for the sample data set) and click the Open button at the bottom of the figure. Next, a Functional Image Information window will pop up (as below) allowing you to enter the image acquisition parameters for the functional scans. Fill all the fields with the values given above (see Section 1.5).
After filling in the correct values in all the fields, press the OK button at the bottom of the window. Next, the Structural Image Information window will pop up (as below) to allow you to enter the necessary structural image parameters.
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Press the (top center) continuation button […], a File Selection dialog will be brought up for user to select file from the list, then it will fill in the filename as well as the pathname automatically. Refer to the structural image acquisition parameters (Section 1.5 above) and enter the correct values in the other fields of this window. Keep the Flip Image checkbox checked. This will flip the images to the neurology standard (“right is right”). If the sequence of structural images begins with the slice closest to the top of the head, check the Re-sort Image checkbox. This will convert the images to begin with bottom slice (as per the requirements of SPM99) for spatial normalization and visualization. The completed window should look like that shown below.
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2.4 Save the FMRLAB dataset
To save the dataset you have just created, select Dataset > Save Dataset from the FMRLAB menu. A file selection window will pop up allowing you to input the output filename. Be sure to append the extension .fmr to the output dataset file. Then, click the “Save” button to save the dataset to disk.
2.5 Remove initial ‘dummy’ scans
The number of dummy scans was specified during the create-dataset procedure (see 2.3 above). To remove those scans from the fMRI time series, select Process > Remove Dummies from the menu.
2.6 Perform slice timing adjustment
To adjust the slice timing (using interpolation to make the acquisition times for the slices as synchronous as possible), select Process > Slice Timing. A Slice Timing Window will pop up (as below) allowing you to specify the sequence in which the functional slices were acquired. There are four possible selections: Interleaved, Ascending, Descending and User Defined. The default is Interleaved.
To use User Defined mode, enter the actual slice sequence, for example, “2 4 6 8 10 1 3 5 7 9,” into the text entry field of the Slice Timing Window. Then press OK to start the slice timing adjustment
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process. During this process, a progress-bar window will pop up to indicate its progress. When the timing adjustment process is done, FMRLAB will close both the Slice Timing Window and the progress bar.
2.7 Remove Off-Brain Voxels
To remove off-brain voxels from the ICA training data, select Process > Extract Brain from the menu. The Extract Brain Voxels window will pop up. Before you start the voxel removal process, press the Preview button (bottom right) to load the functional images.
The images will be displayed in the top row of the window. The bottom row shows the results of using the (not-yet specified) voxel intensity threshold. The figure below shows the Extract Brain Voxels window after the functional images are loaded. The whole functional images are displayed in the first row. Because the threshold (appearing in the text entry field at the bottom of this window) is 0, the thresholded images shown in the bottom row are identical to the whole (top) images.