There are 4 different file types you will encounter in this manual: the GLI files, the TAG files, the GEOM files and the Script files.

 

 

The GLI Files

 

GLI stands for Grey Level Image. It is a generic term used to describe the input images you read in Baby SliceO. The pixel values of these images represent the physical properties of the scanned tissue (CT number, photon emission...) expressed in a numerical form by an 8, 16 or even 32 bit integer. They have a range of values that is usually in the thousands (potentially from -32,768 to 32,767 for a 16 bit image). These images will be displayed in shades of grey, hence the term Grey Level Image or GLI.

 

This program can work with any type of images (CT, MRI, US, SPECT, PET...). But since there are a variety of file formats, some image formats may not be recognized by Baby SliceO. 

 

Presently, Baby SliceO is able to read the following standard formats:

 

DICOM, NEMA-1, NEMA-2, TIFF, JPEG, Interfile 3.0.

 

Also, Baby SliceO is able to read a number of proprietary file formats. A detailed list is available at: http://www.tomovision.com/products/format_image.htm

 

 

The TAG Files

 

The program will help you create a new set of images called TAG images. There will be one TAG image for each GLI image. They contains pixels whose values can range from 0 to 255. These values are tags that are used to identify the anatomical structures of the corresponding pixel in the GLI images.   (ex: all pixels whose tag is 1 are bone, 2 are fat, 3 are muscle ... Or, 1 are kidney, 2 are liver, 3 are bone...).

 

The program will display these TAG images as color images superimposed on the GLI images. Depending on the color scheme selected:

·only the TAG images will be displayed

·only the GLI images will be displayed

·the TAG images will be opaque and displayed over the GLI images

·the TAG images will be translucent and displayed over the GLI images.

 

These new TAG images can be saved in files. The created files will have the same name as the corresponding GLI file but with a ".tag" extension. Optionally, a suffix can be appended at the end of the file. This can be useful if you want multiple users to segment the same GLI images. Each user can have his own suffix and thus have different TAG files while sharing the same GLI files.

 

The format of these files is given in Appendix B: The TAG File Format. 

 

 

The Script Files

 

Reading, sorting and changing the orientation of all the slices of a data set can be a long task. Baby SliceO can help you automate this task by generating a script file. Baby SliceO can generate for you a script file that contains all the information necessary to reread all the files currently in Baby SliceO. Alternatively, you can write your own scripts and use them to read and manipulate your data sets. The syntax of these files is given in Appendix A: The Command line Syntax.

 

 

The Save Data Files option

 

When you click on the Save data Files option, the program will automatically create 3 new files in the same directory as your original file.  A .scp file containing a script of all the module's setups, a .gli file containing the edited GLI values in the orthogonal re-sliced voxels, and a .tag file of the associated TAG masks.

 

When Baby SliceO loads a GLI file, it will automatically search for these 3 associated files.  If found, it will ask you if you want to re-load them. Do not attempt to load these files directly, this will only confuse Baby SliceO.

 

 

The Geom Files

 

Baby SliceO is used to create and manipulate 3D polygonal surfaces. These surfaces can be exported in a number of 3D formats: STL, MOVIE.BYU, DXF, OBJ and VRML.