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View structural and functional MR images with FSLeyes

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Michelle Voss edited this page Oct 19, 2023 · 12 revisions

By the end of this practical you should be able to:

  • use the terminal to navigate to where your MRI data for this course will be
  • open MR images with fsleyes
  • distinguish between structural and functional images in contrast, resolution, and dimensions
  • use fsleyes to identify the coordinates and intensity at the cursor location, and toggle images on/off
  • view the timeseries of a functional image

Access FastX through the remote login:
https://fastx.divms.uiowa.edu:3443/

First prep step, make a folder for holding data for our labs:

  • Open your terminal by clicking on the icon showing a little black screen
  • Type pwd. Where are you in the computer filesystem?
  • Type ls. What other files are here?
  • To make a new folder using the terminal type mkdir fmriLab

Second prep step, download some images:

  • Copy/paste wget -O lab01_images.tar.gz https://osf.io/bprq5/download/
  • Use commands introduced above to see what was downloaded
  • To unpack the download copy/paste tar -xvf lab01_images.tar.gz
  • Move yourself into the folder with data by typing cd osfshare

Open fsleyes:

  • Open fsleyes by typing fsleyes &
  • The & at the end tells the terminal to run this program in the background, meanwhile you still have access to the terminal to run other commands

Open an image with fsleyes:

  • Click on File -> Add from file
  • Open the file named sub-97-T1w_defaced.nii.gz

Understanding the T1 image: Try to answer these questions with your neighbors

1.0. "defaced" means the face has been removed from the image, why do you think we did that?
1.1. What kinds of tissues are the brightest and darkest?
1.2. Place your cursor at different places in the image and see how it affects coordinates
1.3. In addition to the coordinate location of your cursor, what additional information is being shown here?
1.4. How many dimensions are there in the image?
1.5. What do the letters on the four sides of each view shown below mean?


Add a functional image on top of the structural:

  • Use steps learned from above to add a new image
  • Add the file named sub-97_task-flanker_bold.nii.gz
  • Place cursor in the brain somewhere and then toggle on/off the functional image using this button Introduction-to-FSLeyes_toggle-eye-fsleyes

Try to answer these questions with your neighbors

2.0. Does the functional image have more or less anatomical detail than the structural T1 image?
2.1. What kinds of tissues are the brightest and darkest?
2.2. How many dimensions are there in the functional image?
2.3. Use the menu at the top-left of your screen to view the BOLD timeseries for a voxel: View -> Time Series. How does the timeseries compare inside vs. outside the brain.

  • Example with timeseries viewer on:
    Introduction-to-FSLeyes_time-series

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