ROI Toolbox Docs

Documentation: Contrast Movie of Images (biac_movie.m)
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Paul Mazaika
10/01/04

1. Summary
        Displays bulk data for quick visual review by a user. Typical
    time to process and display all the data in 100 scans of size (64,64,30)
    is a minute or two. Every voxel of scan data can be seen. The program does
    not filter the data in any way - rather it lets the user view whether the
    data has unusual artifacts or other characteristics.
        Each scan is made into a montage of slices with orientation
    chosen by input. Any orientation is possible. If the program recognizes
    the orientation of the scanned slices, that option will be starred since it
    is usually the most helpful for viewing artifacts. The montage may be all 
    slices or about 25 consecutive slices viewed twice as large. 
        The slice displays may either be raw image data or contrast
    mode or high contrast mode. The contrast modes show the difference between
    each image and a reference image, amplified so that small data variations
    are more visible. The reference image is the second image in the range.
         In slider mode, every scan montage is available by selecting the 
    slider position. The volumes are labeled, so the user can identify outlier
    scans. The intensity of individual voxels can be examined using the zoom
    button in the Matlab toolbar. In movie mode, every scan
    montage is shown, followed by a time history of mean intensity of each scan.
     
2. Usage
   Choose Orientation:  Transverse, Sagittal, or Coronal.
       For raw images, a * marks the orientation of slice collection.
   Choose a Set of Images (in .img format) to review.
   Choose a Range of images to process. 
       Hundreds of images can be chosen, but the program runs slower.
   Select All slices, or 25 close-up slices.
       In close-up mode, about 20-25 consecutive slices are shown in a
       montage at twice the image size per slice. Select your desired 
       center slice of the montage.
   Select Raw or Contrast or High Contrast display. 
       Raw shows the image data in the set of scans. 
       Contrast shows the difference of the image from a reference scan. The
          reference is the second scan in the range of scans.
          The display shows yellow as higher, and blue as lower from the 
          reference. Values are amplified to be 5x more sensitive for viewing.
          Contrast mode helps to see artifacts in raw images.
       High Contrast is the same as Contrast, but amplified 20x more
          sensitive than raw for a close look at voxel noise.
   Select Movie & Time History,  or interactive Slider.
       If a movie, select a movie frame rate. Three loops are played.
          1 or 2 fps is slow enough to visually spot artifacts.
          At the end of the movie, a time history of the average intensity 
          and position of each scan is displayed.
       The slider shows individual frames and allows user to zoom in and out.
           
3. Outputs
   The reference image, automatically chosen as 2nd in the selected range.
   A movie of a montage of slices, for all the scans of data, 
          followed by a time history plot, OR
   An interactive slider display with all frames of the montage movie.

4. Notes
    Left-Right is not well-defined on the output images.
    Out of Memory error message may occur for large numbers of scans.
        Reduce the number of scans, or close other running programs.
    The reference scan will show as solid black in contrast viewing.

 See also:  spm_movie,  AnalyzeMovie
