Editing VOL

A '''VOL''' primitive represents a three-dimensional grid of cells, also referred to as voxels, which are each either solid or empty. It is defined by a three-dimensional array of unsigned char values (read in from a binary file), where each value represents a cell that is solid if the value lies between the primitive's given upper and lower thresholds, inclusively.

Information about the creation of a VOL primitive using '''in''' is available in the [[BRL-CAD Primitives#vol | list of primitives]].

==Inserting volumetric data of a CT scan in MGED ==

Stanford hosts an [http://graphics.stanford.edu/data/voldata/ archive of volumetric data] for testing purposes.

For this example, let's use the first set of data: "CT study of a cadaver head". It contains 113 files of two-dimensional data with a resolution of 256x256. Each file represents one slice, so we'll need to concatenate them into one file to be able to import it into MGED. In addition, the data is in the form of 16-bit unsigned integers, so we'll need to use '''cv''' to convert it into unsigned chars.

First, download the archive and extract its contents into a directory, which we'll call ''scanslices'':

 $ wget http://graphics.stanford.edu/data/voldata/CThead.tar.gz
 $ mkdir scanslices
 $ tar -zxvf CThead.tar.gz -C scanslices

===Formatting the data===

Next, concatenate them into one file, ''scandata16'':

 $ cat $(ls -v scanslices/*) > scandata16

Convert ''scandata16'' from 16-bit little-endian unsigned integers to big-endian unsigned chars using '''cv''' and write the data to ''scandata8'':

 $ cv hu16 nuc scandata16 scandata8

=== Importing into MGED ===

The data in ''scandata8'' should now be ready to be imported into MGED.

 mged> in
 Enter name of solid: scan
 Enter solid type: vol
 Enter name of file containing voxel data: scandata8
 Enter X, Y, Z dimensions of file (number of cells): 256 256 113
 Enter lower threshold value: 8 255
 Enter X, Y, Z dimensions of a cell: 1 1 1
 
 ERROR: bad pointer 0x1cd74f0: s/b rt_ebm_internal(xf901b231), was rt_vol_internal(x987ba1d0), file /home/jordi/Escriptori/brlcad-7.24.2/src/librt/primitives/vol/vol.c, line 760
 
Whoops. I must have done something wrong.