Reorient Stack (Reorient3_TP)
Author: J. Anthony Parker, MD PhD (
Dates: 2002/05/02: First version
2002/07/10: Pick point options added
2002/07/23: New view from picked points added
2004/07/10: Support for 32-bit floating data added
2010/12/12: Updated to fix crashing
2011/10/03: Added "Read picks" option
Source: Several source files are included in Align Stacks
Installation: Download instructions are in Align Stacks.
Description: Reorient3_TP is one of the ImageJ plugins in the "Align Stacks" directory.  It allows the user to reorient the current stack.  (The current stack is selected by clicking on it.)  Axial, coronal, and sagital view may not make sense prior to reorientation.  Suggestions welcome.

The "Save picks" option defaults to filename "Results.xls"; however, it is stored as a text format file, not in Excel format.  The "Read picks" option reads a text file.  Any line in which the last three tokens are valid numbers are considered the x, y, z values of a pick.  Thus, a Results.xls file will work; a text file with only 3 numbers per line will also work.  If you enter these values with Excel, make sure to save the spreadsheet as text.

Reorient3_TP defaults to a stack orientation which goes from inferior to superior (right handed).  Install with and Arguement which contains "Left", for stacks which go from superior to inferior.  Install with an Arguement which contains "About", to show the about message.

To recompile, make sure the "Align Stacks" folder is in the ImageJ classpath, then just use ImageJ's "Compile and Run ..." option.  (Utility classes are in the package, align3tp, in the "Align Stacks" directory.)

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