1. Medical Image File Formats and Converters
MBI Data Tutorial
7 June 2012
Amanda Ng

2. Outline DICOM HDF5 MINC Analyze/NIfTI RAW DaRIS built-in converters
FILE FORMATS
CONVERTERS
DICOM
HDF5
MINC
Analyze/NIfTI
RAW
DaRIS built-in converters
Matlab
ITK
dcm2nii (MRICron)
MRTrix
MRConvert
MIPAV

3. Image file formats (general)
Consists of:
Metadata (information about the data, eg file size, image dimensions, scan date, patient id)
Data (usually big long string of bytes)
Organised as:
Header (metadata) followed by data
Containers (each has an identifier, metadata, data)
Header
Data
352
EOF
bytes
Example: NIfTI file format
Container
Example: DICOM file format
Tag
Data Type
# elements
Data

4. Medical image file formats
Lots of information Only data
DICOM
HDF5
MINC
NIfTI
Analyze7.5
RAW

5. DICOM Digital Imaging and Communications in Medicine
File format and network communications protocol
Developed/maintained by ACR/NEMA
Current version is 3.0 (since 1993), however updates are released and numbered according to year.
Container-based format
ACR = American College of Radiology
NEMA = National Electrical Manufacturers Association

6. DICOM Advantages Disadvantages
Store infinite amount (well, a lot) of metadata
Easily appendable
Recognised by most software packages (eg Matlab, SPM, MRTrix, MPIAV, Freesurfer)
Usually in the form of a converter to the native format
Except FSL. Grrr…
3D volumes are usually stored as separate DICOM files for each slice
Metadata repeated in every file
100 slices means 100 separate files … ewww
For multi-volume datasets (eg fMRI, diffusion) manufacturers implemented custom embedding of 3D volumes in single files.

7. Value Representation (VR)
DICOM …
Data Element
DICOM file
Data Element
Tag
Value Representation (VR)
Value Length (VL)
Value Field
Tag
Unique Id
Index to the DICOM dictionary
Even numbers are standard (eg Patient Name)
Odd numbers are ‘user defined’ (eg Siemens CSA entry)
VR Description
AE Application Entity
AS Age String
AT Attribute Tag
CS Code String
DA Date
DS Decimal String
DT Date/Time
FL Floating Point Single
FD Floating Point Double
IS Integer String
LO Long String
LT Long Text
OB Other Byte
OF Other Float
OW Other Word
PN Person Name
SH Short String
SL Signed Long
SQ Sequence of Items
SS Signed Short
ST Short Text
TM Time
UI Unique Identifier
UL Unsigned Long
UN Unknown
US Unsigned Short
UT Unlimited Text
Value Length
Number of values in ‘Value Field’
VL > 1 for arrays (eg voxel dimensions)
Value Field
Contains actual metadata

8. Browsing Data Elements
Most DICOM packages have facility to browse data elements or “metadata”
(DCMTK) dcmdump
dcmdump 0001.dcm | grep ‘Manufacturer’
(python) pydicom
import dicom
ds = dicom.read_file(‘0001.dcm’)
ds[0x ]
ds.Manufacturer
Most important data element: Pixel Data
7FE0 0010 OW 1 …
Tag VR VL
Value Field

9. HDF5 Hierarchical Data Format
“data model, library and file format for storing and managing data”
Not medical image specific
Container based format (sort of)

10. HDF5 MINC2 Advantages Disadvantages general self-describing
unlimited *cough* amount of metadata
can embed compressed data
still require some sort of convention for storing medical data (eg metadata fields that should be included, such as voxel size)
MINC2

11. HDF5 Format (basic) … … … HDF5 File Data Descriptor
Data Descriptor Block
Block Size
Offset to Next Block
Data Descriptor …
Every DD Block is the same size. Usually 16 descriptors, but can be changed.
Data Descriptor
Tag
Reference #
Offset
Length 2 4 8 12
HDF File Header
Data Descriptor Block
Data Descriptor Block …
Data Element
Data Element …

12. MINC Medical Image NetCDF
Originally (1992) an extension to the NetCDF file format specific for medical imaging purposes
Reworked into MINC2 in 2003 because of huge datasets, based on HDF5 format
Advantages
Disadvantages
All the HDF5 advantages! Woo!!
Loads of metadata
Doesn’t seem to be well supported by non-MNI applications.
Some software doesn’t support MINC2

13. NIfTI/Analyze 7.5 Analyze 7.5 NIfTI Created by Mayo clinic
Considered old and superseded by Mayo Clinic
Header + data format (but in two separate files)
Ambiguous/limited support for orientation schemes
NIfTI
Specified by NIH
Modified Analyze 7.5 format (backward compatible)
Extended header
Single file
Also an SPM version of NIfTI

14. NIfTI Advantages Disadvantages
Recognised by many software packages (including FSL! Yay!)
Stores translations from patient to image space.
Although facility to extend the header, not usually done and therefore limited in the metadata contained
Limited to 7 dimensions

15. Dim 3 (slices in a volume)
Analyze 7.5 Format
Header Key
Dimensions
History
(description)
(aux_file)
Orientation …
Number of dimensions
Dim 1 (voxels in a row)
Dim 2 (rows in a slice)
Dim 3 (slices in a volume)
Dim 4 (time points)
Dim 5
Dim 6
Dim 7
Datatype
Bits per pixel
Voxel width
Voxel height
Slice thickness …
Size of Header
(data type)
(db_name)
(extents)
(session_error)
(regular)
(hkey_un0)
Header
Orientation
Dim 1
Dim 2
Dim 3
Transverse unflipped
R  L
P  A
I  S
Coronal unflipped
Sagittal unflipped
Transverse flipped
A  P
Coronal flipped
S  I
Sagittal flipped
Data

16. NIfTI changes Header is 4 bytes longer
Optional extended header (though not yet used)
History section of header different
Specifies translation between patient space and image space
Quaternion representation (rotation matrix and offsets), or
Affine matrix representation
Complete set of data types
Standardised storage of data
Dual (.hdr, .img) or single (.nii) file storage

17. Raw Binary Files No header, just the data. Need to know
The dimensions of the data
The datatype (integer, float) and datatype size (8 bit, 16 bit, 32 bit)
Endian-ness
Ordering of the data
Column-major order
Row-major order

18. File Format Support Software DICOM MINC Analyze NIfTI RAW Matlab ✔
EMMA
File XΔ
SPM
via Matlab
FSL ✖
MNI Tools
MRTrix
MPIAV
FreeSurfer
MRICron
ITK
Python
pydicom
nibabel

19. Converters DaRIS built-in converters Matlab MRIConvert MIPAV ITK
dcm2nii (MRICron)
MRTrix

20. DaRIS built-in converters
Datasets stored as
Can convert to
DICOM
Analyze (neurological)
Analyze (radiological)
MINC
NIfTI
Siemens Spectrum
Doesn’t play nice with Skyra frames data *sad face*
Doesn’t appear to convert translation matrix to MINC.
Issues with translation matrix in NIfTI

21. Matlab Can read in these Can write these DICOM NIfTI/Analyze MINC RAW
HDF5 …
NIfTI
DICOM
MINC
RAW
HDF5 …
Reads Skyra data fMRI/Diffusion data! *happy face*
Not straight-forward click-a-button (may need to download files from file exchange)

22. Converts these formats
MRIConvert
Converts these formats
to these formats
DICOM
FSL NIfTI
SPM Analyze
Meta Image
NIfTI
Analyze 7.5
BrainVoyager
Doesn’t play nice with Skyra frames data *sad face*
Creates bvec and bvals files for FSL Diffusion Toolkit *happy face*
Comes with command line version “mcverter”

23. MIPAV Opens these formats Saves these formats DICOM Analyze NIfTI MINC
… others
DICOM
Analyze
NIfTI
MINC
… others
Opens Skyra frames data!!! *big happy face*

24. Other converters dcm2nii (comes with MRICron) ITK MRTrix
Converts DICOM to all forms of NIfTI
Has a GUI
ITK
Sounds amazing! I’m yet to install and play.
MRTrix
Diffusion imaging package
Easy to use command line converter (mrconvert)

25. File Format Links HDF5 MINC MRTrix NIfTI Analyze 7.5
Basic format outline
e_html/UG_Fundmtls.html
Detailed format description:
MINC
MRTrix
NIfTI
Analyze 7.5