DTI Gradient Configuration

Note: The DTI Gradient Configuration dialog can be displayed by clicking on the Edit configuration ... button of the Diffusion Tensor Imaging tab of the Diffusion Analysis dialog box.

This dialog can be used to manually specify the diffusion gradient directions for a given DTI input dataset in the case where this information was not available from the DICOM header. There are various standard configuration setups commonly used by the different MR vendors, which can be found under 3 individual tabs for respectively PHILIPS, GE and SIEMENS scanners. In addition, a Custom tab enables the user to load and manage various customized configurations.

Gradient directions matrix: Table showing the current defined diffusion gradient directions. Each row corresponds to a image in the dynamic sorted image stack, i.e. the first row corresponds to the first image in every slice, the second row to the second image in every slice and so on. By clicking on a given row, the image window holding the input images will be updated to show the image which the row corresponds to. By clicking on the button ("…") at the right of each row a popup menu will appear:

This menu can be used to manual edit the configuration matrix:

Insert 'Excluded image'...: Inserts a "EXCLUDED" image entry either at the current selected row ('here') or at the last row of the table ('last').

Insert 'b=0' image...: Inserts a b=0 image entry either at the current selected row ('here') or at the last row of the table ('last').

Duplicate table (add repetitions) ...: Duplicate the table in two or more (up to six) repetitions. This option can be used if the input dataset holds multiple repetitions of the same DTI sequence.

Delete this entry: Delete the current selected row from the table.

Clear table: Clear (delete all entries) from the table.

b-Value: The b-value used in the diffusion weighted images (only 1 b-value can be specified).

Remember this configuration: Add the current defined (gradient directions & reference frame and b-value) configuration to the list of Predefined configurations. This will save the configuration to a internal configuration file, allowing the configuration to be applied also in subsequent sessions. When doing this, you will be prompted to type a description that will be used to identify the configuration. Whenever the DTI-module is launched on a dataset, the list of Predefined configurations will be searched for a match, i.e. if the number of images per slice corresponds to the number entries in the gradient table, this configuration will be automatically loaded. The name of the configuration will then be displayed in the Current configuration field in the Diffusion Tensor Imaging tab.

Predefined configurations: Drop-down menu holding the configurations previously defined by the user. When you click the Remember this configuration button, the current configuration will be saved and the configuration will be added to this menu.

Delete: Delete the currently selected configuration from the Predefined configurations menu.

Delete all: Delete all configurations from the Predefined configurations menu.

Override header information: Let the user defined configurations override any information that might be extracted from the DICOM header. This is useful if e.g. the information written by the scanner in the DICOM header is not correct, and you always want the Predefined configurations to be used as default.

Import from file: Import/load a configuration from a text-file. The input file format must consist of one direction vector per line; i.e

0, 0, 0

0.8944, 0.0000, -0.4473

0.0000, -0.4473, -0.8945

0.4472, -0.8945, 0.0000

...

where (0,0,0) corresponds to a b=0 image. Specifying the vector (100,100,100) will cause the corresponding image to be EXCLUDED from the analysis. The number of entries in the table must match exactly the number of images per slice in the input dataset, and that the first entry corresponds to the first image, the second entry to the second image and so on.

Export to file: Export/save the current configuration to a text-file.

Edit gradient directions reference frame: Displays the panel showing the transformations that will be applied to the gradient directions prior to the analysis. This can be used to specify the reference frame of which the gradient directions are defined, as this may vary depending of MR vendor and the protocols used. For fiber tracking it is important that the directions are transferred to the image (voxel) coordinate system prior to the analysis.

DTI Gradient Configuration

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