FID Load Option

 

  
Figure 8: FID format options popup window

For loading an image set with fid format[6], the options are shown in Figure 8. The fid can only have a single phase encode and must have the slcto or pss parameter set. The following is a list of steps for specifying options for the loading of an image with fid format:

1. The first step in loading a fid image is to specify the spatial and temporal parameters. When the popup window comes up, the (8-1) and (8-2) fields are set to the indices that yield the full spatial extent of the image volume. Thus the first plane is set to 0 and the last plane is set to the number of planes minus one. For stim files the temporal range is specified by the (8-3) and (8-4) fields, and by default are set to yield the full temporal range. A subset of the data can be specified by modifying the planar and temporal range. As anat files are only 3D spatially, the last time field is not displayed, but the first time can be used to select a particular volume out of a 4D data set.
2. As fids require FFT processing, there are several processing options available. When the option (8-6) is selected, the fid can be buffered to any size that is a power of two in either or both of the (8-7) or (8-8) planar dimension. The (8-5) field displays the planar buffer size as it is modified.
3. When there is a DC offset in the fid data, the post-FFT image will exhibit a bright spot in the center of the image. Since the fid decays to zero at the borders of the image, an effective correction method is to take an average of the fid tails and subtract this average from the entire pre-FFT image. By selecting the option (8-9), the number of complex points along the read out direction ( 8-10) and the phase encode ( 8-11) direction for the tail average can be specified. An average complex value is calculated from points in each corner. Thus the average from these (4 x pe Len x ro Len) points is subtracted from every point in each planar image prior to the FFT.
4. If it is desired to reduce high frequency noise, a gaussian filter can be used by selecting the option (8-12). Then prior to the FFT, the fid image is multiplied by a 2D gaussian with a FWHM (Full Width - Half Maximum) equal to half of the image dimension. Specifically, a 256x256 gaussian image is used and is resized by linear interpolation to the dimensions of the fid image.
5. Normally the magnitude of the complex FFT result is desired. However, under certain experimental situations it may be desirable to use another complex component. The menu under the button (8-13) allows the option of magnitude, phase, real or imaginary to be chosen.
6. When loading stim image files, the (8-14) option is available. When this option is selected, the image volume(s) specified for loading are appended across time to the currently loaded stimulation set of image volumes. Note that the new image volumes to be appended must have the same spatial dimensions as those currently loaded.
7. Lastly, when all the options are set, press the button (8-15) to invoke the loading process. See Section 7 for the procedure to display the images.