Dicom conversion for DTI data
In this page we present some results on the conversion from dicom data to DTI. Working with this new dataset, we noticed differences between the dicom header information and the ones from the original protocol designed for this study. In this page, we want describe and discuss these differences.
The data we worked with have been acquired with a Siemens 3T Tim Trio.
The DTI sequence is a 25 directions with variable b-values plus one B0 image.
We loaded this dicom dataset into the “Dicom DWI loader” module in Slicer3. This module creates a NRRD header based on the information read from the dicom header. We compared the values outputted by the Slicer3 modules with the ones gave to us by the people who designed the DTI sequence.
The protocol specifies a bvalue maximum of bMax = 1000. Then the bvalue for each directions is bMax times the square of the gradient direction magnitude.
We found out that the bvalues that we read from the dicom header are rounded up to the nearest 50. However people from Siemens told us that the actual bvalues used for the acquisition are the correct ones. The bvalue is modified only when written in the dicom header. It seems that if a user does not have the protocol, it's not possible to find to proper, exact bvalues.
We noticed a major difference in the gradient direction encoding. When displaying the original vectors, they seem to be spread around the sphere. Whereas when we display the gradients of the dataset we worked with, they seem to be only on half of the plan. (in blue on the image)
We know that it's not the vector itself which is important for the tensor computation, but more the line held by the vector. When we display lines instead of vectors, we can see that most of the blue lines have a matching red line. There is no more than 3 degrees difference between the vectors.
But the actual values read from the dicom being different from the original sequence could be an issues for some kind of DTI processing.
All the information for the image orientation are included in the dicom header. They are used to create the Nrrd header to process the dwi images. When displaying the tensor we can see that the orientation is not correct. There is a flip along the X axis.
Here are the Nrrd header generated from dicom and its associated tensor visualization:`
NRRD0005 # Complete NRRD file format specification at: # http://teem.sourceforge.net/nrrd/format.html type: short dimension: 4 space: right-anterior-superior sizes: 26 96 96 81 space directions: none (-1.97917,0,0) (0,-1.97917,0) (0,0,-2) kinds: list domain domain domain endian: little encoding: gzip space origin: (48,48,40.5) measurement frame: (1,0,0) (0,1,0) (0,0,1) modality:=DWMRI DWMRI_b-value:=1000.000000 DWMRI_gradient_0000:=0.000000 0.000000 0.000000 DWMRI_gradient_0001:=0.999310 -0.026261 -0.026261 DWMRI_gradient_0002:=-0.935465 0.003956 -0.353397 DWMRI_gradient_0003:=-0.935257 0.004295 0.353943 DWMRI_gradient_0004:=-0.808036 0.528933 0.259437 DWMRI_gradient_0005:=-0.576658 0.580108 -0.575274 DWMRI_gradient_0006:=-0.577350 -0.584657 -0.569950 DWMRI_gradient_0007:=-0.577350 -0.581504 0.573167 DWMRI_gradient_0008:=-0.497275 -0.852931 0.158826 DWMRI_gradient_0009:=-0.354696 0.934976 0.003268 DWMRI_gradient_0010:=-0.355116 0.934819 0.002524 DWMRI_gradient_0011:=0.309152 -0.857266 -0.411728 DWMRI_gradient_0012:=0.305705 -0.000966 0.952126 DWMRI_gradient_0013:=-0.307754 0.002441 0.951463 DWMRI_gradient_0014:=0.002371 0.527850 0.849334 DWMRI_gradient_0015:=0.001497 0.852692 -0.522412 DWMRI_gradient_0016:=0.005889 0.359783 -0.933016 DWMRI_gradient_0017:=0.002612 -0.359715 -0.933057 DWMRI_gradient_0018:=-0.307108 -0.853200 -0.421585 DWMRI_gradient_0019:=0.499156 0.528391 -0.686765 DWMRI_gradient_0020:=-0.499365 0.528606 -0.686448 DWMRI_gradient_0021:=0.496297 -0.854716 0.152151 DWMRI_gradient_0022:=0.577350 -0.581702 -0.572966 DWMRI_gradient_0023:=-0.807921 -0.529384 -0.258876 DWMRI_gradient_0024:=-0.809373 -0.002040 0.587291 DWMRI_gradient_0025:=-0.809376 -0.001631 -0.587289
If we switch the “measurement frame” from (1,0,0) (0,1,0) (0,0,1) to (-1,0,0) (0,1,0) (0,0,1) (flipping the X axis) the tensors “look right” and we can track fibers.
We just wanted to point out here the differences between the information embedded in the dicom header and the one inputted in the scanner when the sequence is designed.