FslBet

FslBet is a Java gui wrapper for the FSL 3.0 bet program. BET (Brain Extraction Tool) deletes non-brain tissue from an image of the whole head. It can also estimate the external skull surface.

For more information about the FSL package, see the FSL (FMRIB Software Library) homepage.
FSL documentation for bet..
Man page to the bet application.

Invocation

java  FslBet

java GlobalDesktop
java GlobalWorkBench
java FslToolChest

FslBet window

Information to be entered

• Input image directory/file
  Use the drop down menu to select an input type, and then use browse to select your input image files. Input types are as follows:
  • File: this allows one file to be selected as input.
  • Directory: this allows a directory to be selected as input. All analyze images (.img/.hdr) in the directory will be run through bet.
  • File List: this allows an ASCII file list to be selected as input; each filename listed in the list will be run through bet.
• Output
  • Output image directory/file
    Directory or filename in which you want the output images to be created in. If a directory is chosen, then the new file created will be called the same name as the input file. If the output directory is the same as the input directory, and no file is chosen, the file name created will be called the filename with "_bet" added to it (eg: input is /home/usr/struct8, then output will be /home/usr/struct8_bet.)
  • Image types
    At least one of these must be checked.
    • brain (-n)
      This option generates a segmented brain image sans skull. It is the default output in the command line.
    • brain overlay (-o)
      This option generates a skull outline overlaid onto the original input image.
    • brain mask (-m)
      This option generates a binary brain mask (0 outside of the brain and 1 inside). This can then be used in later processing, to mask other images derived from the original.
    • exterior skull (-s)
      This option generates an estimate of the exterior surface of the skull. All non-skull-surface points are 0 in this image, and skull-surface points are 100.
• Threshold gradient (-g)
  This option toggles the -g flag in the command line. The default threshold gradient is 0; changing it causes a gradient to be apply to the previous threshold. Setting a positive value here causes the primary threshold to be reduced at the bottom of the brain, giving a larger brain estimate there, and a smaller estimate of t. This value must be in between -1 and 1. More than one threshold gradient can be specified in the box, seperated by spaces. In this case, output file names are also concatenated with "_g0.0", 0.0 being the value input, for example. Below is an example of multiple values input into the text field.

  0.0 0.5 1

• Fraction intensity threshold (-f)
  Changing the fractional intensity threshold from its default value of 0.5 will cause the overall segmented brain to become larger (<0.5) or smaller (>0.5). The range of this threshold is between 0 and 1. More than one fractional intensity threshold can be specified in the box, seperated by spaces. In this case, output file names are also concatenated with "_f0.5", 0.5 being the value input, for example. Below is an example of multiple values input into the text field.

  0.5 0.3 0.2

• Apply thresholding (-t)
  This option causes BET to apply thresholding to the segmented brain image (and also the brain mask if selected). Thus, inside the estimated brain, some voxels can be "zeroed" after segmentation, if their intensity falls below an automatically estimated threshold.
• Verbose output (-v)
  This option produces a more detailed output from the command line.
• Expert Options...
  This button toggles the Expert Options panel that allows access to additional controls.
  • Change coordinates of center of image (-c {x}{y}{z})
    This checkbox enables the float fields for x, y and z to be edited.
  • ... x y z axes (mm)
    Each box represents the coordinates of the center of the images to be created, x, y and z axes respectively. Inputs are float numbers, in millimeters.
  • Radius of image (mm) (-r {r})
    Allows a value for the radius of the output images. Float numbers in millimeters.
• View results
  This option allows for image montages of the output to be displayed and JPEG format images to be created of the montages. Due to memory limitations, not all images are displayed. In order of importance, overlay images are displayed, then brain images, then binary mask, then skull.

• Menubar
• Toolbar
• Output window