About

WARNING The current Canon DICOMs (18 Sept, 2020 V6.0SP2000*) do not report phase encoding polarity, and does not adjust the reported gradient directions with respect to phase encoding polarity. The included series 9000 and 10000 illustrate this issue. This means that the FSL-format bvec files created will incorrect for AP acquisitions: the polarity of the y-component must be inverted. This is a limitation of the images, not the conversion software. If you use DSI Studio, you should select the Check b-table function. If you use FATCAT you should run GradFlipTest. For FSL and other tools, you will need to compensate for this issue.

dcm_qa_canon is a simple DICOM to NIfTI validator script and dataset to test conversion of Canon (né Toshiba) diffusion tensor imaging. Specifically, to ensure that the DICOM gradient vector direction are transformed to match the FSL standard. Note that different vendors use different conventions to report gradient directions. The goal is to convert these to FSL's bvec format which is in image space.

The images were acquired on a Canon Galan 3T by Clément Debacker at Le Groupe Hospitalier Universitaire Paris.

Inspection of the DICOM header tags reveals that these images do not report diffusion gradients in typical tags. Rather, the gradient direction is inserted into the image comments field. The gradient orientation appears to reflect coordinates with respect to the scanner bore (like Siemens, Philips and UIH), rather than the image space (like GE):

 (0018,9087) FD 1500                                     #   8, 1 DiffusionBValue
 (0020,4000) LT [b=1500(0.445,0.000,0.895)]              #  26, 1 ImageComments

The provided dataset adjust the acquisition orientation (axial, coronal, sagittal) and the image angulation. The rationale is to identify whether an image-space or world-space frame of reference is used, and to ensure that these are accurately transformed to FSL's image space format. A dedicated document describes this procedure.

Series

• 9000_DTI_PA-ortho

  • Description: Axial acquisition with no angulation (image space aligned to world). posterior to anterior phase encoding.

• 10000_DTI_AP-ortho

  • Description: Axial acquisition with no angulation (image space aligned to world). anterior to posterior phase encoding.

• 11000_DTI_PA-SAG_20d

  • Description: Sagittal acquisition with 20-degree angulation, posterior to anterior phase encoding.

• 12000_DTI_PA-AX_20d

  • Description: Axial acquisition with with 20-degree angulation, posterior to anterior phase encoding.

• 13000_DTI_PA-COR_20d

  • Description: Coronal acquisition with with 20-degree angulation, posterior to anterior phase encoding.

• 14000_DTI_PA-ALL_20d

  • Description: Sagittal acquisition with 20-degree angulation in each dimension (yaw, pitch, roll), posterior to anterior phase encoding.

• 32000_DTI_PA-ortho-HT

  • Description: Axial acquisition with no angulation (image space aligned to world), posterior to anterior phase encoding. Head turned of about 45 degrees on the right.

• 33000_DTI_PA-ortho-HT-VT

  • Description: Axial acquisition with angulation to match anatomy), posterior to anterior phase encoding. Head turned of about 45 degrees on the right.

• 37000_SAG_DTI_PA-ortho

  • Description: Sagittal acquisition with no angulation (image space aligned to world). posterior to anterior phase encoding.

• 38000_SAG_DTI_PA-COR_20d

  • Description: Sagittal acquisition 20-degree angulation, posterior to anterior phase encoding.

• 39000_SAG_DTI_PA-ALL_20d

  • Description: Sagittal acquisition with 20-degree angulation in each dimension (yaw, pitch, roll), posterior to anterior phase encoding.