MouseBIRN.MBATFileFormats (r1.1 vs. r1.6)
Diffs

 <<O>>  Difference Topic MBATFileFormats (r1.6 - 27 Apr 2006 - HengYuan)

META TOPICPARENT MBATWorkPage
jboline - 01 Mar 2006
Line: 78 to 78

 of Ivo's LOVE program. Therefore some .bgx files contain fields that are ignored by the MBAT BrainGraph file filter.
Added:
>
>		 .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)
Line: 95 to 114
META FILEATTACHMENT MAP2003_256.bgx.txt attr="" comment="" date="1143564971" path="MAP2003_256.bgx.txt" size="15883" user="SteveAnderson" version="1.1"
META FILEATTACHMENT MAP2003_256.label.lbl attr="" comment="" date="1143565123" path="MAP2003_256.label.lbl" size="51915" user="SteveAnderson" version="1.1"
META FILEATTACHMENT MAP2003_256.label.atlas attr="" comment="" date="1143565148" path="MAP2003_256.label.atlas" size="253" user="SteveAnderson" version="1.1"
Added:
>
>
META FILEATTACHMENT MAP2003_256.ilf attr="" comment="" date="1146100737" path="C:\heng\pjcvs\atlas\MAP2003_256.ilf" size="10955" user="heng" version="1.1"

 <<O>>  Difference Topic MBATFileFormats (r1.5 - 28 Mar 2006 - SteveAnderson)

META TOPICPARENT MBATWorkPage
jboline - 01 Mar 2006
Line: 6 to 6

.hdr

Changed:
<
<		 It is the header file of an Analyze(tm) image volume, which cotains two parts, a header file and a raw image file (with .img extension).
>
>		 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.
Changed:
<
<		 MBAT will attempt to look for the .img or .img.gz file with the same prefix as the raw image data file.
>
>		 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

Changed:
<
<		 It is the raw image data file of an Analyze(tm) image volume, which cotains two parts, a header file (with .hdr extension) and a raw image file.
>
>		 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).
Deleted:
<
<		 MBAT will attempt to look for the .hdr file with the same prefix as the header file.

.label.hdr (MAP2003_256.label.hdr). .label.img (MAP2003_256.label.img).

Changed:
<
<		 An Analyze image volume that indicates its purpose as a label volume. Usually There is also an label text file (.lbl extension) associated with label volume to indicate the meaning of each intensity value in the volume.
>
>		 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).

Changed:
<
<		 An Analyze image volume that indicates its purpose as a mask volume. It is usually unnecessary for finished set of image volumes, but it is usually used to either to protect specific regions from being changed, or to set certain
>
>		 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

Changed:
<
<		 A fairly common 2D image file format. It may contain a single slice of image, typically from a scanner. Or it may contain a stack of images,
>
>		 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

Changed:
<
<		 for medical image volumes. MBAT is able to read GZIP compressed file (with .mnc.gz extension) as well.
>
>		 for medical image volumes.

File Management

.keg

An XML file containing a list of files to be loaded at the same time.

Changed:
<
<		 It also offers the ability to adjust coordiniate of image volumes.
>
>		 It also offers the ability to adjust the coordinates of image volumes. MAP2003_256.atlas

Changed:
<
<		 .atlas (MAP2003_256.atlas)
>
>		 .atlas (MAP2003_256.atlas)

Changed:
<
<		 The format is exactly the same as .keg a file, but MBAT treats label and mask image volume files as read only.
>
>		 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

Changed:
<
<		 .bgx (MAP2003.bgx)
>
>		 .bgx (MAP2003_256.bgx.txt)

Changed:
<
<		 This is a BrainGraph file in XML. It contains a list of anatomical
>
>		 This is an XML BrainGraph file. It contains a list of anatomical

structures and their relationships (typically hierarchical relationship).

Typically, it contains

Line: 76 to 74
  • abbrev ("CTX")
  • full name ("Cerebral cortex")
Changed:
<
<		 .bgx file was originally derived from BrainGraph file in .gml format, which was part of Ivo's LOVE program. Therefore some .bgx files contain more fields, most of which are ignored by MBAT BrainGraph file filter.
>
>		 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.

.lbl

Changed:
<
<		 .label.lbl
>
>		 .label.lbl (MAP2003_256.label.lbl)

Changed:
<
<		 Text index file associated with the label image file. For each
>
>		 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.
Changed:
<
<		 .label.atlas (MAP2003_256.label.atlas).
>
>		 .label.atlas (MAP2003_256.label.atlas).

Changed:
<
<		 This is used by MBAT to load different atlas label image volume and label text files associated with each atlas.
>
>		 This is an XML file similar to the .atlas file but it used specifically for label image volumes.

Added:
>
>

META FILEATTACHMENT MAP2003_256.atlas attr="" comment="" date="1143564914" path="MAP2003_256.atlas" size="425" user="SteveAnderson" version="1.1"
META FILEATTACHMENT MAP2003_256.bgx.txt attr="" comment="" date="1143564971" path="MAP2003_256.bgx.txt" size="15883" user="SteveAnderson" version="1.1"
META FILEATTACHMENT MAP2003_256.label.lbl attr="" comment="" date="1143565123" path="MAP2003_256.label.lbl" size="51915" user="SteveAnderson" version="1.1"
META FILEATTACHMENT MAP2003_256.label.atlas attr="" comment="" date="1143565148" path="MAP2003_256.label.atlas" size="253" user="SteveAnderson" version="1.1"

 <<O>>  Difference Topic MBATFileFormats (r1.4 - 08 Mar 2006 - HengYuan)

META TOPICPARENT MBATWorkPage
jboline - 01 Mar 2006
Line: 9 to 9

 It is the header file of an Analyze(tm) image volume, which cotains two parts, a header file and a raw image file (with .img extension). The format specification is at http://www.mayo.edu/bir/PDF/ANALYZE75.pdf.
Added:
>
>		 MBAT will attempt to look for the .img or .img.gz file with the same prefix as the raw image data file.

.img .img.gz

Line: 17 to 19

 two parts, a header file (with .hdr extension) and a raw image file. 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).
Added:
>
>		 MBAT will attempt to look for the .hdr file with the same prefix as the header file.

.label.hdr (MAP2003_256.label.hdr). .label.img (MAP2003_256.label.img).

Line: 38 to 42

A fairly common 2D image file format. It may contain a single slice of image, typically from a scanner. Or it may contain a stack of images,

Changed:
<
<		 converted by ImageJ?.
>
>		 converted by ImageJ?. MBAT can read both.

.mnc .mnc.gz

Changed:
<
<		 A popular 3D image volume format based on NetCDF for medical image volumes.
>
>		 A popular 3D image volume format based on NetCDF for medical image volumes. MBAT is able to read GZIP compressed file (with .mnc.gz extension) as well.

Changed:
<
<

Other Files

>
>

File Management


.keg

Line: 57 to 63

 The format is exactly the same as .keg a file, but MBAT treats label and mask image volume files as read only.
Added:
>
>

Other Files


.bgx (MAP2003.bgx)

This is a BrainGraph file in XML. It contains a list of anatomical

Line: 84 to 92

 This is used by MBAT to load different atlas label image volume and label text files associated with each atlas.
Deleted:
<
<

File Management


 <<O>>  Difference Topic MBATFileFormats (r1.3 - 07 Mar 2006 - HengYuan)

META TOPICPARENT MBATWorkPage
jboline - 01 Mar 2006

Image Files

Changed:
<
<		 .atlas (MAP2003_256.atlas)
>
>		 .hdr

Changed:
<
<		 An XML index containing the name of the other files that comprise that atlas (.dwz.img, .label.img, .mask.img, label.lbl. and .bgx). This file also provides the starting (x, y, z) coordinates of the 3-D display.
>
>		 It is the header file of an Analyze(tm) image volume, which cotains two parts, a header file and a raw image file (with .img extension). The format specification is at http://www.mayo.edu/bir/PDF/ANALYZE75.pdf.

.img .img.gz

It is the raw image data file of an Analyze(tm) image volume, which cotains two parts, a header file (with .hdr extension) and a raw image file. 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).


Changed:
<
<		 .bgx (MAP2003.bgx)
>
>		 .label.hdr (MAP2003_256.label.hdr). .label.img (MAP2003_256.label.img).

Changed:
<
<		 An XML file containing hierarchical data about individual anatomical structures and sub-structures. In the .bgx files I've looked at, this information consists of the following items for each structure (node).
>
>		 An Analyze image volume that indicates its purpose as a label volume. Usually There is also an label text file (.lbl extension) associated with label volume to indicate the meaning of each intensity value in the volume.

Changed:
<
<
  • numerical index
  • full name ("Cerebral cortex")
  • abbrev ("CTX")
  • description (empty in the files I've seen)
  • bounding box coordinates for the structure
  • a description of the "image" used to display the node in the BrainGraph viewer. In MBAT this is ignored and the node is drawn as a simple oval.
  • 3D (x, y, z) atlas coordinates for the location of the center of the structure. These coordinates are NOT in the same space as those in the .atlas file. They are apparently transformed internally by MBAT.

The .bgx file also contains additional "edge" data that defines the relationship of the nodes to each other.

Ivo implied that .gml files (on which .bgx is based) can contain additional information, such as links to data files and external databases. I haven't seen such information in any existing .bgx files but, I can see no reason this information could not be included in .bgx files.

.dwz.hdr (MAP2003_256.hdr)

A header file for the .dwz.img file below. Seems to contain additional header information that cannot be included in the .dbz.img file itself.

.dwz.img (MAP2003_256.dwz.img).

A binary image file containing a series of 2D pixel image slices that constitute a 3D image (a "data volume"). I believe Heng mentioned that these files are usually in Analyze Image format, but MINC and ImageJ? TIFF files can also be displayed.

>
>		 .mask.hdr (MAP2003_256.mask.hdr). .mask.img (MAP2003_256.mask.hdr).

Changed:
<
<		 .label.atlas (MAP2003_256.label.atlas).
>
>		 An Analyze image volume that indicates its purpose as a mask volume. It is usually unnecessary for finished set of image volumes, but it is usually used to either to protect specific regions from being changed, or to set certain regions to blank.

Changed:
<
<		 This XML file contains file and coordinate references similar to the the .atlas file. It may be redundant and unnecessary.
>
>		 .tif .tiff

Changed:
<
<		 .label.hdr (MAP2003_256.label.hdr). .mask.hdr (MAP2003_256.mask.hdr).
>
>		 A fairly common 2D 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?.

Changed:
<
<		 Small binary header files. I'm not sure of their purpose.
>
>		 .mnc .mnc.gz

Changed:
<
<		 .label.img
>
>		 A popular 3D image volume format based on NetCDF for medical image volumes.

Changed:
<
<		 Another type of binary image file, similar to .dwz.img, but also containing label information ("a label volume"). I dont have any information about the format of the label image file.
>
>

Other Files


Added:
>
>		 .keg

An XML file containing a list of files to be loaded at the same time. It also offers the ability to adjust coordiniate of image volumes.

.atlas (MAP2003_256.atlas)

The format is exactly the same as .keg a file, but MBAT treats label and mask image volume files as read only.

.bgx (MAP2003.bgx)

This is a BrainGraph file in XML. It contains a list of anatomical structures and their relationships (typically hierarchical relationship).

Typically, it contains

  • numerical index
  • abbrev ("CTX")
  • full name ("Cerebral cortex")

.bgx file was originally derived from BrainGraph file in .gml format, which was part of Ivo's LOVE program. Therefore some .bgx files contain more fields, most of which are ignored by MBAT BrainGraph file filter.

.lbl


.label.lbl

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.

Changed:
<
<		 .mask.img
>
>		 .label.atlas (MAP2003_256.label.atlas).

Changed:
<
<		 Similar to dwz.img but used as a "mask volume" rather than a data volume
>
>		 This is used by MBAT to load different atlas label image volume and label text files associated with each atlas.

File Management


 <<O>>  Difference Topic MBATFileFormats (r1.2 - 03 Mar 2006 - SteveAnderson)

META TOPICPARENT MBATWorkPage
jboline - 01 Mar 2006

Image Files

Added:
>
>		 .atlas (MAP2003_256.atlas)

An XML index containing the name of the other files that comprise that atlas (.dwz.img, .label.img, .mask.img, label.lbl. and .bgx). This file also provides the starting (x, y, z) coordinates of the 3-D display.

.bgx (MAP2003.bgx)

An XML file containing hierarchical data about individual anatomical structures and sub-structures. In the .bgx files I've looked at, this information consists of the following items for each structure (node).

  • numerical index
  • full name ("Cerebral cortex")
  • abbrev ("CTX")
  • description (empty in the files I've seen)
  • bounding box coordinates for the structure
  • a description of the "image" used to display the node in the BrainGraph viewer. In MBAT this is ignored and the node is drawn as a simple oval.
  • 3D (x, y, z) atlas coordinates for the location of the center of the structure. These coordinates are NOT in the same space as those in the .atlas file. They are apparently transformed internally by MBAT.

The .bgx file also contains additional "edge" data that defines the relationship of the nodes to each other.

Ivo implied that .gml files (on which .bgx is based) can contain additional information, such as links to data files and external databases. I haven't seen such information in any existing .bgx files but, I can see no reason this information could not be included in .bgx files.

.dwz.hdr (MAP2003_256.hdr)

A header file for the .dwz.img file below. Seems to contain additional header information that cannot be included in the .dbz.img file itself.

.dwz.img (MAP2003_256.dwz.img).

A binary image file containing a series of 2D pixel image slices that constitute a 3D image (a "data volume"). I believe Heng mentioned that these files are usually in Analyze Image format, but MINC and ImageJ? TIFF files can also be displayed.

.label.atlas (MAP2003_256.label.atlas).

This XML file contains file and coordinate references similar to the the .atlas file. It may be redundant and unnecessary.

.label.hdr (MAP2003_256.label.hdr). .mask.hdr (MAP2003_256.mask.hdr).

Small binary header files. I'm not sure of their purpose.

.label.img

Another type of binary image file, similar to .dwz.img, but also containing label information ("a label volume"). I dont have any information about the format of the label image file.

.label.lbl

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.

.mask.img

Similar to dwz.img but used as a "mask volume" rather than a data volume


File Management


 <<O>>  Difference Topic MBATFileFormats (r1.1 - 01 Mar 2006 - JylBoline)
Line: 1 to 1
Added:
>
>
META TOPICPARENT MBATWorkPage
jboline - 01 Mar 2006

Image Files

File Management


Topic: MBATFileFormats . { View | Diffs | r1.6 | > | r1.5 | > | r1.4 | More }

Revision r1.1 - 01 Mar 2006 - 02:04 - JylBoline
Revision r1.6 - 27 Apr 2006 - 01:08 - HengYuan