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Run Stamp  start time       Sat Apr 26 10:51:17 2008
           machine name     3dma.ams.sunysb.edu
           operating system Linux
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Input Data Options
	simulated data (0)
	tomographic data (1)
	segmented data (2)
	burn data (3)
	medial axis data (4)
Enter choice: 4

Data Processing Options
	plot MA (1)
	convert MA files to segmented file type (2)
	convert MS files to segmented file type (3)
	histogram and fit pore MA burn data (4)
	embed search tree(s) (5)
	shortest paths (6)
	min cut/max flow (7)
	convert data to/from ascii format (8)
	convert MA list to/from node/path formats (9)
	modify MA (10)
	histogram MA info (11)
	reconstruct fibers (12)
	fiber width by MoI (13)
	fiber width by MoI - simple (14)
	free fiber ends (15)
Enter choice: 10

    Files assumed to be labelled  basename.ext,
    basename  is limited to 255 characters maximum,
    ext       is a numerical designator lying between 000 and 999
    It is assumed that the files have consecutively numbered extensions
        ie.  000 -> 056,  or   021 -> 049

Enter basename for Medial structure file(s): ../ma/fbr
Are file(s) compressed? [y,n]: y
Enter basename for burn file(s): ../burn/fbr
Are file(s) compressed? [y,n]: y

Resize information selection.
NOTE, row and column numbers begin from 0

For each slice,
   enter first and last column of data to use (x-dir): 0 511
   enter first and last row of data to use (y-dir): 0 511

enter first and last slice of data to use (z-dir): 1 10

Trim medial structure voxels on volume edges? (y,n(dflt)): y

Medial axis clean up control menu

	Maximum burn number on medial axis is 4

    Remove isolated voxels (y,n(dflt)): y
	Remove isolated voxels having burn number less than: 10

    Remove isolated paths (y,n(dflt)): y
	Remove isolated paths having length less than: 2000

    Remove branch-leaf paths (y,n(dflt)): y
    Retain branch-leaf paths exiting through boundary? (y,n(dflt): y
    branch-leaf path removal criteria
	Remove path if length less than
		maximum cluster burn number (auto)
		user specified tolerance    (user)
	Enter choice (a(dflt),u): u
	Enter tolerance length: 5

    Remove needle-eye paths (y,n(dflt)): y
    needle-eye path removal criteria
	Remove path if length less than
		maximum cluster burn number (auto)
		user specified tolerance    (user)
	Enter choice (a(dflt),u): u
	Enter tolerance length: 10

    Surface Remnant clean up
	Reduce surface remant structure where possible(y,n(dflt)): y

Enter voxel length in physical units: 7

Specify output medial axis data format
	voxel location list only (v)
	cluster/path format      (cp)
	graph node/path format   (g)
Enter format (v,cp,g): cp

Merge close clusters? (y,n(dflt)): n

Enter basename for singlet loc/burn file(s): ../ma_t/cp_sngl
Enter basename for cluster/path loc/burn file(s): ../ma_t/cp_loc
Enter basename for cluster/path structure file(s): ../ma_t/cp_struct
Are file(s) to be compressed? [y,n]: y