RAW Load Option

  
Figure 10: Raw format options popup window

For loading an image set with raw format, the options are shown in Figure 10. There are two modes for loading a raw image set, dependent on whether the or choice (10-10) is selected. For the File mode, the raw format is the same as the sdt format, except that it doesn't have a companion spr file. See Appendix A for a discussion of sdt format. For the Directory mode, a set of sequentially numbered planar image files can be loaded to form a volume or set of volumes.

1. The first step in loading a raw image is to specify the spatial and temporal parameters. The (10-1), (10-2) and (10-3) fields specify the horizontal, vertical and depth dimensions respectively, in units of pixels. For each of these spatial dimensions, the corresponding field of view must also be indicated ( 10-21). Similarly, a value must be entered in the field (10-4) to indicate the temporal extent of the data set. These fields must be set such that they yield the full spatial and temporal extent of the data.
2. If the entire data set is to be loaded, the spatial and temporal range must be set to the full extent. Thus the field (10-5) must be set to 0 and the field (10-6) must be set to one less than the number of planes given in (10-3). Similarly the field (10-20) must be set to 0 and the field (10-19) must be set to one less than the number of volumes given in (10-4).

   A subset of the data can be specified by modifying the planar and temporal range. The planar range is modified by setting the (10-5) and (10-6) fields. For stim files the temporal range is specified by the (10-20) and (10-19) fields. 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.

3. When loading stim image files, the option (10-18) 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.
4. One of the choices (10-7) must be selected as described in Table 12. An orientation (See Table 4) must be specified for the data and can be set with the choice (10-8). If the planar orientation of the images does not conform to one of the orientation choices, two options are available to flip and/or rotate the images about their centers. The choice (10-9) allows for either a horizontal or vertical flip, and the (10-17) option allows for any arbitrary rotation. Note that if both options are specified, the flip is performed before the rotation.
5. When the choice (10-10) is selected, there are five additional fields displayed. The first field, (10-16) specifies the number of bytes, if any, at the beginning of each file that should be skipped prior to reading image data. The remaining four fields specify the pattern for the names of the files to load. The pattern is composed of a file number preceded by the string specified by the (10-11) field and terminated by a dot (``.'') and the string specified by the (10-12) field: {Prefix}{File Number}.{Extension}

   The file numbers are the inclusive sequential set between the (10-15) and the (10-14) field values. Note that all zeros in the file number of a file name are ignored. For example, the file number strings ``001'' and ``1'' are equivalent. Table 3 gives a list of files that would be loaded for the values given in the fields of Figure 10.

6. Lastly, when all the options are set, press the button (10-13) to invoke the loading process. See Section 7 for the procedure to display the images.