FSL analysis

Background

[Image: fsl's tabs]

Expected brain activation.

Consider a simple experiment where we ask an individual to press their left hand at some timepoints, their right hand at other times, and to simply rest at other moments in time. In this situation one would expect that the left motor cortex and right cerebellum will be activated following right hand movement. This tutorial shows how to analyze this dataset. Below we provide a sample dataset, but the brain imaging center includes an e-prime script (”12secOn12secOff”) and a scanning sequence (in the “/rorden/basic” folder) so you can collect your own data.

The image below illustrates our study. The vertical axis shows time, in 2 second fMRI volumes (so the experiment takes just over six minutes). The red and green bars along the top of the image show when the individual presses their left (red) or right hand (green) – note that they press the same hand continuously for 12 seconds (a ‘block’ design). The red and green lines show the predicted blood flow signal for regions that are activated following left and right hand movements. Note that we expect the images to become brighter several seconds after an individual starts a task (the blood flow effect is sluggish).

[Image: Model Timecourse]

Analyzing the dataset

    [Image: fsl's tabs]

    FSL’s tabs.

  1. get the file 20090430_152500.zip from the web server.
  2. uncompress the zip file (on OSX, double click on the archive). This archive contains a fMRI dataset (fmri12secon12secoff.nii.gz), an anatomical scan (t1.nii.gz), and text files reporting the onset of the left and right hand movements (left.txt, right.txt). The images are in FSL’s favorite NIfTI format. Alternatively, you can download the raw DICOM data from our scanner.
    Since FSL can not read DICOM data, you will need to convert these files with dcm2niigui.
  3. Drop one of the extracted files (e.g. MR.1.2.13…) onto dcm2nii to convert (for OSX, drop the file on the program’s icon in the dock).
  4. dcm2nii will create .nii.gz files, once it is done you can delete the MR.1.2… files
  5. Launch a terminal window, use cd to change the directory to the newly created .nii.gz files, e.g. “cd ~/desktop/mr”
  6. In the command line, type “FSL &” to launch FSL.
  7. Press “FEAT fMRI analysis tools”.
  8. Data tab:
    • press “select 4D data” and choose the fMRI dataset (this should have ‘S003″ in the name, as it was the 3rd session. Note that once you have selected the file, the “total volumes” will list 188.
    • Set the TR(s) to be 2.0, as we collected one volume every 2 seconds.

      10.) Pre-stats tab – keep all the defaults, except set the spation smoothing to 8mm and click on the Lowpass filter (as this is a block design).

  9. Stats tab -
    • press full model setup for GLM window (steps c..d)
    • set number of original EVs to 2
      Tab “1″ set EV name to “left”, basic shape to “Custom (3 column format) and set the filename to the left.txt file. Uncheck “add temporal derivative” (as this is a block design).
      Tab “2″ set EV name to “right”, basic shape to “Custom (3 column format) and set the filename to the right.txt file. Uncheck “add temporal derivative” (as this is a block design).

    • Contrasts and F-tests tab : set Contrasts to 2, for the OC1, set the Title to “L>R” and set EV1 = “1″ and EV2 = “-1″, or the OC2, set the Title to “R>L” and set EV1 = “-1″ and EV2 = “1″
    • press “Done” on GLM window
  10. Press “Go”
  11. When FSL has completed, it will generate a web page that reports the results.