View source for NAMIC Wiki:DTI:DICOM for DWI and DTI

This page should serve as a place where information about DICOM and DWI/DTI data can be maintained. With time, this information could be used as part of automated solutions for learning all the necessary DWI-related information from a DICOM series. A collection of tools for DICOM is [[DICOM|here]].

As long DICOM support for DWI information is vendor-specific and/or non-conformant with the info here, the [[NAMIC_Wiki:DTI:Nrrd_format|Nrrd format ]] provides a means of recording the DWI-specific information once it is known.

== DICOM for DWI ==

The recommended tags to use in DICOM are as follows:

 0018 9075 CS 1 Diffusion Directionality
 0018 9076 SQ 1 Diffusion Gradient Direction Sequence
 0018 9087 FD 1 Diffusion b-value
 0018 9089 FD 3 Diffusion Gradient Orientation
 0018 9117 SQ 1 MR Diffusion Sequence
 0018 9147 CS 1 Diffusion Anisotropy Type

These are defined in [ftp://medical.nema.org/medical/dicom/final/sup49_ft.pdf Supplement 49]. In particular see section C.8.12.5.9 "MR Diffusion Macro" on pages 94 and 95.

The tags are also referenced in http://medical.nema.org/dicom/2004/04_06PU.PDF (see pages 28-29) as well as in some [http://medical.nema.org/Dicom/minutes/WG-07/WG-07_2005/Minutes-2005-10-20-21-Denver.doc Working Group Minutes] (see pages 155-156).

Two points of interest relative to the NRRD format:

* The definition of "Diffusion Gradient Orientation" implies that the measurement frame is exactly the identity transform.
* There appears to be no means of recording the full B-matrix when it is known. This is not an issue for any NAMIC datasets, but can arise in small-bore imaging.

=== Private vendor: GE ===

For GE scanners, Signa Excite 12.0 and later, the following tags are reserved for diffusion weighted images:

* (0019,10e0) : # DTI diffusion directions (release 10.0 & above)
* (0019,10df) : # DTI diffusion directions (release 9.0 & below)
* (0019,10d9) : Concatenated SAT {# DTI Diffusion Dir., release 9.0 & below}
* (0021,105A) : diffusion direction
* (0043,1039) : Slop_int_6... slop_int_9: (in the GEMS_PARM_01 block)
** 6: b_value
** 7: private imaging options 2
** 8: ihtagging
** 9: ihtagspc

This information can be found in http://www.gehealthcare.com/usen/interoperability/dicom/docs/5162373r1.pdf

Unfortunately the [[DataRepository|Dartmouth DWI data ]] (from a GE Signa scanner) does not conform to this (nor do they use the nominally standard 0x0018 tags), as can be seen by running:

 dcdump S4.100 | & grep \(0x0019,0x10

which includes:

 (0x0019,0x10d9) DS Concatenated SAT      VR=<DS>   VL=<0x0008>  <0.000000>
 (0x0019,0x10df) DS User Data     VR=<DS>   VL=<0x0008>  <0.000000>
 (0x0019,0x10e0) DS User Data     VR=<DS>   VL=<0x0008>  <0.000000>

so all of the tags which are supposed to store # gradient directions store the value 0! In addition, there is:

 (0x0021,0x105a) SL Integer Slop          VR=<SL>   VL=<0x0004>  [0x00000000]

so the supposed representation of diffusion-direction is also empty. The Dartmouth data has the following tags describing the scanner and software version:

 (0008,1090) LO [GENESIS_SIGNA]
 (0018,1020) LO [09]

In GE DWI images (software version 12.0)

 (0008,1090) LO [SIGNA EXCITE]
 (0018,1020) LO [12\LX\MR Software release:12.0_M4_0520.a]

diffusion directions are stored under the following tags:

 (0019,10bb) DS [0.430617]
 (0019,10bc) DS [-0.804161]
 (0019,10bd) DS [-0.420008]

=== Private vendor: Siemens ===

A Siemens DICOM Conformance Statement is available at

 http://www.medical.siemens.com/siemens/en_INT/rg_marcom_FBAs/files/brochures/DICOM/mr/dcs_trio.pdf

No diffusion related tags specified.

David Tuch has stated (in email from December 21, 2005):

 The diffusion gradient information and coordinate frame are not provided
 in the DICOM hdr for the MGH diffusion sequences.

'''Tag 0029,1010''' may include all necessary information

If you have installed spm (and Matlab), the following spm-File extracts the gradient info:

 
 P= spm_get(Inf,'*','Selct some files')
 hdr=spm_dicom_headers(P)
 hdr{1}.CSAImageHeaderInfo(22).item(1).val
 hdr{1}.CSAImageHeaderInfo(22).item(2).val
 hdr{1}.CSAImageHeaderInfo(22).item(3).val

look for "spm_dicom_headers.m" (google or on your hard disk), this spm File shows you how to decode the tag data.

It is easy to write a C or C++ program that does the same, if you have the spm_dicom_headers.m

Credits: Jan Klein <klein AT mevis DOT de>

==== Update ====

<br /> As far as the latest MR scanner software (2006) version is concerned, a solution for the access of the following Diffusion attributes was provided:

 0019;000A;SIEMENS MR HEADER  ;NumberOfImagesInMosaic          ;1;US;1
 0019;000B;SIEMENS MR HEADER  ;SliceMeasurementDuration        ;1;DS;1
 0019;000C;SIEMENS MR HEADER  ;B_value                         ;1;IS;1
 0019;000D;SIEMENS MR HEADER  ;DiffusionDirectionality         ;1;CS;1
 0019;000E;SIEMENS MR HEADER  ;DiffusionGradientDirection      ;1;FD;3
 0019;000F;SIEMENS MR HEADER  ;GradientMode                    ;1;SH;1
 0019;0027;SIEMENS MR HEADER  ;B_matrix                        ;1;FD;6
 0019;0028;SIEMENS MR HEADER  ;BandwidthPerPixelPhaseEncode    ;1;FD;1

That does not solve your problem with the older datasets and unfortunately there is no easy way to access diffusion information there as it is really only stored in the Siemens shadow part.

Credits: Stefan Huwer

==== User Note ====

Don't use the gradient-directions from the DICOM header from VB13 systems, it commonly contains errors; read the b-matrix instead and use that to compute the gradient-directions. In fact, this is also what Siemens does but they compute the gradient-vectors in an error-prone way. They do (in Matlab syntax):

 % BMtx = [bxx bxy bxz byy byz bzz]
 GradVec = BMtx([1:3])/sqrt(BVal*BMtx([1]));

This gives errors for bxx values of zero and close to one (bxx is an integer); NB this *does* happen! So instead read the b-matrix and do:

 BSign   = sign(sign(BMtx([1:3])) + 0.01);   % Adding 0.01 avoids getting zeros here
 GradVec = BSign .* sqrt(BMtx([1 4 6])/BVal);

In this way, the vectors may point exactly in the opposite direction (sign flip), but this is usually of no importance.

Furthermore, the stored values may differ from the official values due to the fact that
# the directions are calculated from the b-matrix and not directly written to the header. Rounding errors, as well as sign flips may occur in this case.
# the b-matrix takes also the diffusion effect of imaging and spoiling gradients into account. This leads to deviations from the originally specified orientations.
# the vectors are expressed in the patient coordinate system (Sag/Cor/Tra), not in Slice/Read/Phase, following the DICOM convention.

Credits: Marcel Zwiers

==== Reference ====

* http://www.mmrrcc.upenn.edu/CAMRIS/cfn/

in particular:

* http://www.mmrrcc.upenn.edu/CAMRIS/cfn/dicomhdr.html

=== Private vendor: Philips ===

Philips uses the following tags for diffusion weighted images

* (2001,1003) : B_value;
* (2001,1004) : Diffusion direction.

Complete DICOM conformance statements for

* Intera
* Achieva
* Panorama
* Gyroscan
* Infinion / Eclipse

are available here http://www.medical.philips.com/main/company/connectivity/mri/

== DICOM for estimated diffusion tensors ==

There is no specification right now in DICOM to support Tensor. Only a supplement:

[ftp://medical.nema.org/medical/dicom/supps/sup63_pc.pdf Supp 63 Parts 3,4,5,6,16,17 Multi-dimensional Interchange Object ]

The discussion would then be (D. Clunie quote):

 
 Indeed, even if one were to try to standardize in DICOM the encoding
 of the entire diffusion tensor, there would no doubt be considerable
 debate as to whether to do that as 6 (or 9) planes of an "image", since
 there is such a matrix at each spatial location ("pixel"), or as
 a special case of the proposed Sup 63 object; the former would keep
 image-oriented tools and software happier, the latter would require
 implementing a new mechanism and navigating through a more general
 structure.

== Discussion on DICOM newsgroup ==

http://groups.google.com/group/comp.protocols.dicom/browse_frm/thread/3d292d9c506b1cbf For cross reference:

 
 Hi Mathieu
 
 Thanks for the very interesting links.
 
 The proposed standard way to address this problem is with
 the Enhanced MR IOD, which explicitly addresses the
 attributes for encoding diffusion directionality and B-Value.
 
 There will likely be no extensions of the existing MR IOD to
 address this concern, since by policy, we obviously want
 folks to use the new IOD.
 
 It would not surprise me if in the interim, vendors started
 to send some of the new Sup 49 attributes in old IOD
 instances, but there will almost certainly be no official move
 to standardize this, and we would certainly not consider
 adding a non-Sup 49 based mechanism.
 
 If the Sup 49 mechanisms are not sufficient (e.g. for
 tensors), then we need to discuss what the gaps are
 and how to fill them.
 
 We would not, by the way, ever "encapsulate" the NRRD
 header, but it would nice if there was a clear mapping between
 the DICOM Sup 49 attributes and the relevant NRRD
 attributes, though these are probably obvious.
 
 David
 
 Mathieu Malaterre wrote:
 > Hello again,
 >
 >    I am currently involved in a group which is working extensively with
 > DWI data (diffusion-weighted image). Their acquisition data is coming
 > in the form of DICOM files. Unfortunately they are currently facing two
 > problems:
 > 1. Each vendors stores the gradient directions differently (if at all!)
 > 2. Even if you have the directions, you don't have the measurement
 > frame(*). As far as I understand the DICOM specification, there is
 > currently no way to store this type of information.
 >
 >    For issue #1 I am currently gathering information about the major
 > vendors so that I can add extraction code into gdcm. This would provide
 > a function to extract the gradient directions and make invisible to
 > user the different way vendors use to store this information. For more
 > information see the Wiki at:
 > http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
 >
 >    For issue #2, -again correct me if I am wrong- but I could not find
 > anything that could represent this measurement frame. Therefore the
 > solution we are using is to use an intermediate file format called
 > NRRD, see for instance:
 > http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
 >    Ideally this information should be accessible from a particular
 > DICOM tag. Can we request an extension of the DICOM standard to allow
 > us to store this information directly in the DICOM file, which would
 > greatly simplify the process (avoiding the intermediate NRRD file
 > format step).
 >
 > Regards,
 > Mathieu
 > (*)
 > "measurement frame": relationship between the coordinate frame in which
 > the gradient coefficients are expressed, and the physical coordinate
 > frame in which image orientation is defined