Difference between revisions of "NAMIC Wiki:DTI:DICOM for DWI and DTI"

Revision as of 09:57, 5 August 2008

Home < 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 here.

As long DICOM support for DWI information is vendor-specific and/or non-conformant with the info here, the 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 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 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 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>

Another solution is simply to download GDCM 2.x application (gdcmdump) and type:

$ gdcmdump --csa input.dcm

Output should look like:

(0029,0010)siemens csa header
Image shadow data (0029,xx10)

0 - 'EchoLinePosition' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '192     '
1 - 'EchoColumnPosition' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '128     '
2 - 'EchoPartitionPosition' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '16      '
3 - 'UsedChannelMask' VM 1, VR UL, SyngoDT 9, NoOfItems 6, Data '255     '
4 - 'Actual3DImaPartNumber' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
5 - 'ICE_Dims' VM 1, VR LO, SyngoDT 19, NoOfItems 6, Data 'X_1_1_1_1_1_1_1_1_1_1_1_136'
6 - 'B_value' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
7 - 'Filter1' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
8 - 'Filter2' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
9 - 'ProtocolSliceNumber' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '0       '
10 - 'RealDwellTime' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '7500    '
11 - 'PixelFile' VM 1, VR UN, SyngoDT 0, NoOfItems 0, Data
12 - 'PixelFileName' VM 1, VR UN, SyngoDT 0, NoOfItems 0, Data
13 - 'SliceMeasurementDuration' VM 1, VR DS, SyngoDT 3, NoOfItems 6, Data '73375.00000000'
14 - 'SequenceMask' VM 1, VR UL, SyngoDT 9, NoOfItems 6, Data '0       '
15 - 'AcquisitionMatrixText' VM 1, VR SH, SyngoDT 22, NoOfItems 6, Data '256*256'
16 - 'MeasuredFourierLines' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '0       '
17 - 'FlowEncodingDirection' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
18 - 'FlowVenc' VM 1, VR FD, SyngoDT 4, NoOfItems 0, Data
19 - 'PhaseEncodingDirectionPositive' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '1       '
20 - 'NumberOfImagesInMosaic' VM 1, VR US, SyngoDT 10, NoOfItems 0, Data
21 - 'DiffusionGradientDirection' VM 3, VR FD, SyngoDT 4, NoOfItems 0, Data
22 - 'ImageGroup' VM 1, VR US, SyngoDT 10, NoOfItems 0, Data
23 - 'SliceNormalVector' VM 3, VR FD, SyngoDT 4, NoOfItems 0, Data
24 - 'DiffusionDirectionality' VM 1, VR CS, SyngoDT 16, NoOfItems 0, Data
25 - 'TimeAfterStart' VM 1, VR DS, SyngoDT 3, NoOfItems 6, Data '0.00000000'
26 - 'FlipAngle' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
27 - 'SequenceName' VM 1, VR SH, SyngoDT 22, NoOfItems 0, Data
28 - 'RepetitionTime' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
29 - 'EchoTime' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
30 - 'NumberOfAverages' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
31 - 'VoxelThickness' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
32 - 'VoxelPhaseFOV' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
33 - 'VoxelReadoutFOV' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
34 - 'VoxelPositionSag' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
35 - 'VoxelPositionCor' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
36 - 'VoxelPositionTra' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
37 - 'VoxelNormalSag' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
38 - 'VoxelNormalCor' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
39 - 'VoxelNormalTra' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
40 - 'VoxelInPlaneRot' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
41 - 'ImagePositionPatient' VM 3, VR DS, SyngoDT 3, NoOfItems 0, Data
42 - 'ImageOrientationPatient' VM 6, VR DS, SyngoDT 3, NoOfItems 0, Data
43 - 'PixelSpacing' VM 2, VR DS, SyngoDT 3, NoOfItems 0, Data
44 - 'SliceLocation' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
45 - 'SliceThickness' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
46 - 'SpectrumTextRegionLabel' VM 1, VR SH, SyngoDT 22, NoOfItems 0, Data
47 - 'Comp_Algorithm' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
48 - 'Comp_Blended' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
49 - 'Comp_ManualAdjusted' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
50 - 'Comp_AutoParam' VM 1, VR LT, SyngoDT 20, NoOfItems 0, Data
51 - 'Comp_AdjustedParam' VM 1, VR LT, SyngoDT 20, NoOfItems 0, Data
52 - 'Comp_JobID' VM 1, VR LT, SyngoDT 20, NoOfItems 0, Data
53 - 'FMRIStimulInfo' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
54 - 'FlowEncodingDirectionString' VM 1, VR SH, SyngoDT 22, NoOfItems 0, Data
55 - 'RepetitionTimeEffective' VM 1, VR DS, SyngoDT 3, NoOfItems 0, Data
56 - 'CsiImagePositionPatient' VM 3, VR DS, SyngoDT 3, NoOfItems 0, Data
57 - 'CsiImageOrientationPatient' VM 6, VR DS, SyngoDT 3, NoOfItems 0, Data
...

Ref:

http://gdcm.sourceforge.net/wiki/index.php/GDCM_Release_2.0

Update

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/

DTI Table Gradient

OVERVIEW: 

This applet computes the gradient table
for DTI data acquired on Philips MRI
scanners with low, medium, and high 
directional resolution.

The imaging parameters and DTI options
listed can affect the gradient table.
e.g.directions from a gradient overplus
= yes table need to be adjusted for the
slice angulation (i.e. oblique slices)
specific to each DTI study 

The output is appropriate for DTIstudio.
I hope this applet is useful, but please
use it at your own risk. Matlab code with
more functionality is available on my 
webpage

http://godzilla.kennedykrieger.org/%7Ejfarrell/OTHERphilips/GUI.html

DICOM for estimated diffusion tensors

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

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

Difference between revisions of "NAMIC Wiki:DTI:DICOM for DWI and DTI"

Revision as of 09:57, 5 August 2008

Contents

DICOM for DWI

Private vendor: GE

Private vendor: Siemens

Update

User Note

Reference

Private vendor: Philips

DTI Table Gradient

DICOM for estimated diffusion tensors

Discussion on DICOM newsgroup

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