jboline - 01 Mar 2006
Image Files
.hdr
This is the binary header file of an Analyze(tm) image volume. An image
volume contains two files, a header file (.hdr) and a raw image file (.img).
The format specification is at
http://www.mayo.edu/bir/PDF/ANALYZE75.pdf.
When loading a raw image data file (.img or .img.gz),
MBAT will attempt
to look for the the .hdr file with the same prefix as the raw image data file.
.img
.img.gz
This binary file is the raw image data file of an Analyze(tm) image volume.
The format specification is at
http://www.mayo.edu/bir/PDF/ANALYZE75.pdf.
MBAT can read GZIP compressed image data file (with .img.gz extension).
.label.hdr (MAP2003_256.label.hdr).
.label.img (MAP2003_256.label.img).
An Analyze image volume that is intended to be used as a label volume.
There is usually an additional label text file (.lbl extension) associated
with a label volume. The label text file contains a structure label (name
and description) for the intensity values in the volume.
.mask.hdr (MAP2003_256.mask.hdr).
.mask.img (MAP2003_256.mask.hdr).
An Analyze image volume that is intended to be used as a mask volume. This
volume is usually unnecessary for a finished set of image volumes, but it can
be used to protect specific regions from being changed, or to set certain
regions to blank.
.tif
.tiff
A fairly common 2D binary image file format. It may contain a single slice
of image, typically from a scanner. Or it may contain a stack of images,
converted by
ImageJ?.
MBAT can read both.
.mnc
.mnc.gz
A popular 3D image volume format based on
NetCDF
for medical image volumes.
File Management
.keg
An XML file containing a list of files to be loaded at the same time.
It also offers the ability to adjust the coordinates of image volumes.
MAP2003_256.atlas
.atlas (
MAP2003_256.atlas)
The format is exactly the same as .keg a file, but will treat the
listed label and mask image volume files as read only.
Other Files
.bgx (
MAP2003_256.bgx.txt)
This is an XML
BrainGraph file. It contains a list of anatomical
structures and their relationships (typically hierarchical relationship).
Typically, it contains
- numerical index
- abbrev ("CTX")
- full name ("Cerebral cortex")
The .bgx format was derived from the
BrainGraph .gml format that was part
of Ivo's LOVE program. Therefore some .bgx files contain fields that are
ignored by the
MBAT BrainGraph file filter.
.ilf Integrated Label File (
MAP2003_256.ilf)
This is a simplified version of a full .bgx
BrainGraph file. Instead of specifying
nodes and edges at the separate places, it use nesting of XML tags as
a way to indicate hierarchical relationship. The result is a simpler,
and more intuitive format for hierarchical relationship of brain structures.
The hierarchy can be ignored if one is mainly interested using .ilf as a label
text file replacement.
It contains the following information for each structure
- color value
- numerical index
- abbrev ("CTX")
- full name ("Cerebral cortex")
We are in the process of replacing the separate braingraph and label file formats
with this ILF format.
.lbl
.label.lbl (
MAP2003_256.label.lbl)
A text index file associated with the label image file. For each
structure there is a line containing the unique index number,
color value, abbreviation and full name of that structure.
.label.atlas (
MAP2003_256.label.atlas).
This is an XML file similar to the .atlas file but it used
specifically for label image volumes.
MAP2003_256.atlas 
MAP2003_256.bgx.txt