1. Importing an Image into BioImage Suite

Figure 1

The Import option of BioImage Suite is used in lieu of (File | Load) when the user would like to manipulate the image while loading it or if the user would like to load a different kind of file type other than analyze file format.  Most whole brain sequences for single subjects will appear upside down if loaded using the (File | Load) option.  In order to flip the brain image to show a right-side-up image, the user would choose (File | Import) and choose the option Flip Y before loading.   You may use either pxitclbrainsegment or pxitclbrainregister for all of the following instructions.

  1. Choose OrthoViewer (or BrainSegment) from the BioImage Suite main page.
  2. In the OrthoViewer or BrainSegment window Choose (File | Import) - 
  3. A new Import Image Control window will appear - check to see if the Image File Type is set to Analyze.
  4. If the Image File Type is something other than Analyze you can either change it every time you import a file or you can set the default to be Analyze by going back to the BioImage Suite main window and choose Preferences.
  5. A new Biosuite User Preference window will appear and you can choose the File Formats tab.
  6. Under the Default Import Mode you can toggle the type to be Analyze.
  7. Then choose Save to save your default preferences
  8. Once your Image File Type is chosen properly, you can choose the proper image header file for your 3D wholebrain acquisition.  The Import Image Control window will toggle to the Preferences tab once you select an image header file.
  9. If orientation is sagittal - choose Flip Y (choosing Flip Y will orient the brain so the top of the brain is at the top of the image)
  10. Click Load and update