REGION
Group Voxels into Regions

REGION is a FORTRAN90 library which manipulates 3D voxel data.

As part of a project, we had to take a file of voxel data representing a brain scan. Each voxel had an integer value representing the intensity of a signal. Only voxels with an intensity above a certain value were to be considered. Those voxels were then grouped into contiguous regions.

A further complication was the desire to be able to include an enclosing surface image of the brain, project the internal regions out along a line from a point to the surface, and mark the surface with the color associated with the region. Some of the routines in this package are associated with that task.

A simple routine called IVOXEL_TO_OBJ allows you to take a voxel array and create a corresponding OBJ 3D graphics file.

Licensing:

The computer code and data files described and made available on this web page are distributed under the GNU LGPL license.

Languages:

REGION is available in a FORTRAN90 version.

Related Data and Programs:

ASCII_TO_MRI, a C program which restores MRI data to its original binary format, having been previously converted to an ASCII text file.

IMAGE_COMPONENTS, a FORTRAN90 library which seeks the connected "nonzero" or "nonblack" components of an image or integer vector, array or 3D block.

MRI_TO_ASCII, a C program which reads a (binary) MRI file and makes an ASCII copy that can be handled by REGION.

MRI_TO_PGM, a C program which converts the binary data in an MRI file to a sequence of PGM image files.

OBJ_DISPLAY, a MATLAB program which reads an OBJ 3D graphics file and displays it on the screen.

Source Code:

• region.f90, the source code;

Examples and Tests:

• region_test.f90, the calling program;
• region_test.txt, the output file;
• roi.ascii, the sample data file.
• roi.obj, an OBJ version of the data.
• roi.png, a PNG snapshot of the 3D object.

List of Routines:

• FACE_PRINT prints the nodes that define one face of a voxel.
• GET_UNIT returns a free FORTRAN unit number.
• IVOXEL_BOUND_PRINT writes bounding faces to an OBJ file.
• IVOXEL_COUNT_POSITIVE counts the positive entries in a voxel array.
• IVOXEL_PLOT prints out a typewriter plot of the Z slices.
• IVOXEL_PLOT2 prints out a typewriter plot of the regions.
• IVOXEL_PLOT3 prints out a typewriter plot of data/100.
• IVOXEL_READ reads MRI data from an ASCII file, one item per line.
• IVOXEL_SUM sums the entries in a voxel array.
• IVOXEL_THICKEN "thickens" the voxels.
• IVOXEL_THRESH zeroes out array entries below a given threshhold.
• IVOXEL_TO_OBJ writes out an OBJ file from a voxel array.
• IVOXEL_TO_REGION arranges a set of voxels into contiguous regions.
• IVOXEL_WRITE writes MRI data to an ASCII file, one item per line.
• NODE_PRINT prints the nodes that define one face of a voxel.
• REGION_BLANK zeroes out voxels in a particular numbered region.
• REGION_CENTER computes the centers of mass of the regions.
• RVOXEL_TO_IVOXEL copies real voxel data into an integer voxel array.
• TIMESTAMP prints the current YMDHMS date as a timestamp.
• TRANSPORT transports voxels to the boundary, counts intermediate hits.
• TRANSVOX transports one voxel to the boundary.
• VOXEL_INDEX_STEP computes indices of voxels along a line from a given point.
• VOXEL_NODES returns the indices of the nodes of a voxel.

You can go up one level to the FORTRAN90 source codes.