Artifacts lab

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Artifacts Lab

Susceptibility artifacts

In this exercise you will examine how magnetic susceptibility causes artifacts in fMRI images. You will do this using a feature in FSLView that allows you to view two images alongside one another.

Run FSLView and load the following files from the ~/FSL/additional_data/ directory:

“t1.img” – this is an anatomical image

“epi.img” – this is a functional image

This will put the functional image superimposed on the anatomical image (provided you loaded the anatomical volume first). You can adjust the colormap and transparency levels of both volumes while visualizing these data.

Question: What areas of the brain appear to be affected by susceptibility artifacts in the epi image? Refer to either your printed atlases or to the website from the anatomical practical. Also, can you tell what anatomical feature causes each of these regions to show an artifact?

Head motion

In this exercise you will see the effect of motion correction using MCFLIRT. Subjects tend to move their heads slightly during the course of an experiment. If we do not do motion correction on our images, the position of an area in the brain at the beginning of the experiment does not correspond to the position of that area at the end of the experiment.

The data for this exercise are also in the additional_data directory. The data file is called “motion.nii”. First, view the raw data to see if you can detect motion in the timeseries.

In FSLView, first close any other images you may have open, and then select the motion.nii file from the File->Open menu.

Next, click the Movie mode button, which looks like a section of movie film in the middle of the button bar.

This will display each of the timepoints in the scan consecutively, generating a ‘movie’ of your brain over time.

Based on visual inspection alone, can you see any motion that might introduce artifacts in later analysis if not corrected? If so, in what direction(s)?

Now we will actually run the correction, and see what effect motion correction has on these data.

To run MCFLIRT, FSL’s Motion Correction LInear Registration Tool, we will use the command line. Open a new terminal window by clicking on the X11 icon in the dock, and then selecting “new terminal” from the file menu.

In that terminal, change to the directory where the motion file is located by typing:

cd ~/FSL/additional_data/

Be sure to include the space between the command ‘cd’ and the path. From there, we can run MCFLIRT by typing:

mcflirt –in motion.nii

This tells mcflirt to use the motion file as input. By default, it will add a “_mcf” to the input filename when generating the output. It will also compress the file, so there will be a “.gz” added as well. Load this new file into FSLView like we did with the non-corrected file. What has changed between the two? If you are curious, feel free to explore the various parameters available for motion correction by typing mcflirt -help, which will list all of the options that are user configurable.