DTI pipeline interface

This panel is for uploading DW and T2 images, calculating gradients,uploading B-matrix information, and creating the B-matrix/Gradient table. DTI Pipeline reads raw data in all MIPAV supported formats and DICOM files.

DWI Image Browse – check this option if you would like to upload your image of interest from your computer.

Use Active DWI Image – check this option to use an active image, which is already opened in MIPAV.

Note: in MIPAV, an active image is the one that has a red frame.

This option allows a user to manually upload B-Value/Gradient File or B-Matrix file. See also: Table Options.

Gradient vector file is a 3D set of coordinates representing the direction (on the form of a vector) along which a magnetic gradient has been applied. Each DTI pulse sequence has a set of gradient vectors associated with it. This set is required for subsequent analysis.

B-value is a scaling factor used to describe the attenuating effect of the MR signal on the different gradients. A diffusion gradient can be represented as a 3D vector, where the direction of vector is in the direction of diffusion and its length is proportional to the gradient strength. The gradient strength, or more often used diffusion weighting parameter term, is expressed in terms of the B-value parameter, which is proportional to the product of the square of the gradient strength (q) and the diffusion time interval (b ~ q2 • Δt). Read more: MRI TIP database.

The Philips Gradient Creator computes the correct gradient table which is necessary to calculate diffusion tensors. The table lists gradient vectors that describe the diffusion weighting directions, which are later used for analysis and computing diffusion tensor. The Gradient Creator works with data acquired by Philips MRI scanners. Note: the Philips Gradient Creator options would not appear for images from other scanners.

It uses the source code from DTI_gradient_table_creator created by Jonathan Farrell, Ph.D.

The code that computes the gradient table based on minimal user input. The list of input parameters is show below, see Gradient Creator input parameters. You can also refer to Jonathan Farrell's web site for additional information.

The specifications of the gradient table created for the image taken on Philips MRI scanner(s) are determined by:

• The 3 coordinate frames defined on the MR scanner: world, anatomical, and image coordinate system. For more information, refer to Slicer WIKI.
• The rules on how imaging options (including slice orientation, slice angulation, phase encoding direction, etc.) impact the gradient directions.
• The scanner software release.
• Any motion correction, if performed.

In diffusion tensor imaging (see [1]), tensors are constructed by collecting a series of direction-sensitive diffusion images. MRI scanners save these directions along with the images and later they are used to reconstruct the diffusion properties of the images.

Depending on the scanner, the vectors are recorded with reference either to the scanner bore, or to the imaging grid. This should not a problem if the images are acquired precisely orthogonal to the scanner bore, because in that case the image and the scanner share the same frame of reference.

Problems can arise in oblique acquisitions when the image plane is not aligned with the scanner bore. In this situation, it is important that the gradient vectors used in the imaging software are in the same frame of reference as the image. This requires conversion or re-ordering, otherwise we will get angulation errors.

Note: these angulation errors have little influence on the DTI parameters, which are invariant to tensor rotation - ADC, MD and FA. However, they do affect calculation of the eigenvectors of the tensor.

In the Gradient or B-Matrix table, if gradients are displayed, the 2nd column contains B values, while X Gradient, Y Gradient and Z gradient columns contain the diffusion gradients applied along the x, y, and z axis - Gx, Gy, and Gz correspondingly.

If B-matrix is displayed, 6 b-values are displayed per volume including bxx, byy, bxy, bxz, byz, and bzz.

Gradient Creator Parameters	Options	Philips PAR/REC Version
Fatshift	R: Right L: Left A: Anterior P: Posterior H: Head F: Feet	V3 & V4 V4.1 & V4.2
Jones30 or Kirby	Specify which MRI scanner was used to acquire DW images. This option works for KKI scanners only.	V3 & V4 V4.1 & V4.2
Gradient Resolution	Low: used for 8 DWI volumes Medium: used for 17 DWI volumes High: used for 34 DWI volumes	V3 & V4 V4.1 & V4.2
Gradient Overplus	Yes No	V3 & V4 V4.1 & V4.2
Philips Release	Rel_1.5 Rel_1.7 Rel_2.0 Rel_2.1 Rel_2.5 Rel_11.x	V3 & V4 V4.1 & V4.2
Patient Position	Head First Feet First	V3 & V4
Patient Orientation	SP: Supine PR: Prone RD: Right Decubitus LD: Left Decubitus	V3 & V4
Fold Over	AP: Anterior-Posterior RL: Right-Left FH: Head-Feet/ Superior-Inferior	V3 & V4
OS (Operating System)	Windows VMS	V3 & V4 V4.1 & V4.2 (for KKI scanners only)
Inverted	No Yes	V3 & V4 V4.1 & V4.2 (for KKI scanners only)

Compute Gradient Table - use this button to compute the gradient table based on data you entered into Gradient Input Parameters.