Image Fitting - Input Images

The Image Fitting works with a set of images, representing each of the values of the independent variable. You will normally need to enter the independent variables value corresponding to each image. However, in certain cases, you may be able to find the independent variable values automatically from the image headers. To try this, select . In order for this work, you must have used Jim's Image Converter to create the images, or they must be in DICOM format. Currently, the only variable values that can be extracted from the images are:

• The echo time (TE)
• The repetition time (TR)
• The inversion time (TI)
• The diffusion-weighting b-factor

When setting up the input images, there are two basic options:

• Each value of the independent variable is in a separate image file.
  In this case, select:

  

  Then click on the button until you have the correct number of image selection panels in the "Input images" pane (one for every independent variable value). If you have too many images, you can remove any of them by clicking on the icon.

  For each of the input image panels, set an input image file by clicking on the load image icon: . This will bring up a File Chooser that you can use to set the input image corresponding to the independent variable value on the right. Alternatively, you can simply type in the folder and image file name in the text fields, or you can press the right mouse button and select from the menu of recently-used images. You can also drag-and-drop an image onto the panel.

  For each input image, set the value of the independent variable by typing it into the field to the right of the image name. For example, if you are performing T₂ fitting, and you have images with echo times of 30 and 80 ms, you would type in:

  

  You can work with any number of input images (one per independent variable value) as long as you have at least as many input images as there are fit variables; to work with more images, click on the button until you have the desired number of images in the "Input images" panel.

  All input images must be of the same dimensionality (i.e., the same number of slices, and rows and columns of pixels within the slice).

• All values of the independent variable are in one image file.
  In this case, select:

  

  Set an input image file by clicking on the load image icon: . This will bring up a File Chooser that you can use to set the input image. Alternatively, you simply type in the folder and image file name in the text fields, or you can press the right mouse button and select from the menu of recently-used images.

  Set the values of the independent variable by typing it them as a comma-separated list into the "Independent variables values" field For example, if you are performing T₂ fitting, and you have images with echo times of 30 and 80 ms, you would type in:

  

  Note: The independent variable values must be in the same order that they appear in the input image.

  Next, are the individual slices in your input image ordered with all independent variable values for one slice sequential in the image, or all slice locations for one independent variable sequential? The figure below illustrate these two cases for a double echo sequence with two echo times:

  

  All variable values for one slice location are adjacent in the image. Select:

  

  

  All slice locations for one variable value are adjacent in the image. Select:

  

Having set up the input images, you should now supply the base name for the output images.