Surface/Volume

Some of the values computed by this tool are displayed in this window. If you want access to all the values computed, you need to open a secondary window with the "Window Values" button. You can control which of the values are displayed with the command line. By default, the surfaces and volumes are displayed.

Window Values

Clicking this button will cause a secondary window to be created. This window will contain all the values computed by the tool.

The values computed are:

•"Surface Units", The surface of each TAG in surface units (see the Units tool)

•"Volume Units", The volume of each TAG in volume units (see the Units tool)

•"Surface Pixel", The surface of each TAG in pixels

•"Volume Voxel", The volume of each TAG in voxels

•"GLI Mean", The mean value of the pixel under each TAG in the pixel's units

•"GLI Min", The minimum value of the pixel under each TAG in the pixel's units

•"GLI Max", The maximum value of the pixel under each TAG in the pixel's units

•"GLI SD", The standard deviation of the values of the pixel under each TAG.

The values that are not selected to be saved in the result files will be displayed in grey. This can be changed either from the configuration menu or through the command line.

Only one such window can exist at any time, clicking this button while the window is already created will pop the associated window on top of the other windows.

Window Graph

Clicking this button will cause a secondary window to be created. This window will contain a graph of the surface of each tag on each slice as a function of the slice position in space.

Only one such window can exist at any time, clicking this button while the window is already created will pop the associated window on top of the other windows.

Calibration

If you know what is the relationship between pixel values and something else, you can add a calibration file that will define this relationship. For example, if you know how to compute a tissue density from the CT Housfield units (HU), you can use a calibration file to let the program know about this. In this way, the mean, min and max values will be in densities instead of HU.

Configuration

Clicking this button will open a configuration menu. In this menu you will be able to specify the content and form of the result files you can create from this tool. The configuration menu is described in more detail further down.

Write Result

Create a result file. The results can be either in standard ASCII text, or in a tabulated form compatible with Excel. You can set the default for this with the configuration menu, or changing the "save as type" parameter in the confirmation pop-up window.

File Type

Result files can either be in plain ASCII text (compatible with notepad or any text editors) or in "DB file", a tabulated form, compatible with Excel or most spreadsheet programs.

Headers

You can have 3 optional headers in the files you created:

The Patient Info header

For each patient used in creating the file we will have (if the information is present in the image's header):

•Patient Name          

•Patient ID

•Patient sex

•Date of Birth

•Patient weight (Kg)

•Patient height (m)

The Scanner Info header

For each scanner used in creating the file we will have (if the information is present in the image's header):

•Modality

•Manufacturer

•Model

The Image Info header

For each image used in creating the file we will have (if the information is present in the image's header):

•Resolution X Y          

•Pixel Dim. X Y Z (mm)

•Horiz. Dir. X Y Z          

•Vert. Dir. X Y Z

Saved Measures

You can select which of the available measures you want to save in your result files.

Float Fraction

You can specify whether you want the fractions in your floating point values to be delimited by a dot (".") (example:12.34) or a comma (",") (example: 12,34). By default it is the dot.

Cell Delimiter

You can specify the character you want to use to mark the end of a cell in your spreadsheet result files. By default it is the "tab" character.

Cell Filler

You can specify what should be placed in cells that have no values. For example, in a result file for multiple frames, if a TAG is not present in all the frames, then in some cells we will not have surfaces and volumes for it.

Default Path

You can specify the default path for the results files. There is only one "default path" parameter in sliceOmatic, so by default, this value is set to the path of the last file read or written.

Default Name

You can set a default name for your result files.

Cancel

Close the configuration menu without saving any of the changes you just made.

Accept Changes

Accept the changes you made and close the configuration menu. Please note that these changes only affect the current invocation of sliceOmatic. If you want to save the changes for future invocations of the program, you need to use the "Script Save As..." option of the File menu.

Z_A

= position in Z of the image A

N_A

= number of pixels of a certain Tag value in image A

P_A

= surface of a pixel in image A

S_A

= surface covered by a Tag value on the image A (= N_A P_A)

T_A

= thickness of image A

_AB

= gap or overlap between the two images A and B

V_AB

= volume of a Tag value between the two images A and B

∆ = 0

There is no gap, and the computation of the volume of the Tag value between A and B is straightforward:

V_AB = ½T_AS_A + ½T_BS_B

∆ > 0

There is a gap between the slices and we have to interpolate the volume in the gap. This volume will be approximated by a truncated pyramid joining the volumes of both slices.

V_AB = ½T_AS_A + ½T_BS_B  +  ∆_AB (¹/₃ ABS(S_A - S_B) + MIN(S_A, S_B))

∆ < 0

The images overlap and we have to compute the volume in this overlap region. The volume in the region without overlap is computed as before, and in the overlap we will again use the truncated pyramid.

V_AB = (½T_A + ½∆_AB) S_A + (½T_B + ½∆_AB) S_B

       -  ∆_AB (¹/₃ ABS(S_A - S_B) + MIN(S_A, S_B))

All slices are 10.0 mm thick

All pixels are  0.25 mm²

(T_a to T_D = 10.0)

(P_A to P_D = 0.25)

Image A:

 has 400 pixels of Tag value 1

 is positioned at Z = 100.0

(N_A = 400)

(Z_A = 100.0)

image B:

 has 300 pixels of Tag value 1

 is positioned at Z = 110.0

(N_B = 300)

(Z_B = 110.0)

image C:

 has 500 pixels of Tag value 1

 is positioned at Z = 115.0

(N_C = 500)

(Z_C = 115.0)

image D:

 has 600 pixels of Tag value 1

 is positioned at Z = 130.0

(N_D = 600)

(Z_D = 130.0)

$RESULT_BACKWARD

(U8)

Backward compatibility flag (1=compatible with 4.3)

$RESULT_NAME

(A,S)

Array of result computation name

$RESULT_UNIT

(A,S)

Array of result computation units

$RESULT_ENABLE

(A,C₈)

Array of flag for the display/output of the result computations (0x01=in output file, 0x02=displayed)