Input/Output Data Format

Diffusion Toolkit (DTK) uses Nifti as the default (and recommended) data format.

DTI reconstruction

The input files for DTI reconstruction can be either raw DICOM files or Nifti/Analyze files. It can be a series of single volume image files, or one 4D image file with the 4th dimension as the time point.

The output files of DTI reconstruction include:

• _b0.nii. Averaged low b (b0) map.
• _dwi.nii. Diffusion weighted image map.
• _fa.nii. Fractional Anisotropy (FA) map.
• _fa_color.nii. Color FA map.
• _adc.nii. Apparent Diffusion Coefficient (ADC) map.
• _e1/e2/e3.nii. Eigen value maps. e1 is the largest and e3 is the smallest.
• _v1/v2/v3.nii. Eigen vector data. Each is a standard nifti vector file. (5 dimensions. The size of the 4th dimension (time point) is 1 and the 5th dimension is 3.)
• _tensor.nii. Diffusion tensor data. A 4D nifti file with the 4th dimension size as 6 (6 elements of a diffusion tensor matrix). Will be used as input for tracking program.

DSI/Q-Ball/HARDI reconstruction

The input files for DSI/Q-Ball/HARDI reconstruction can be either raw DICOM files or Nifti/Analyze files. It can be a series of single volume image files, or one 4D image file with the 4th dimension as the time point.

The output files of DSI/Q-Ball reconstruction include:

• _b0.nii. Averaged low b (b0) map.
• _dwi.nii. Diffusion weighted image map.
• _odf.nii. Orientation Distribution Function (ODF) map. This and the max.nii are the two main data file from DSI/Q-Ball reconstruction. The file is a 4D volume, with dimension of 181 * X * Y * Z. X/Y/Z are the dimension of the original raw image volume. 181 is 181 samples of the ODF on pre-defined 181 direction vectors, which cover half semi-sphere. The 181 direction vectors can be found here. ODF file consists of 4 byte float numbers.
• _max.nii. MAX map is also a 4D volume file with the same dimension as the ODF map. But it only contains values of 0 or 1's, serving as a mask for the ODF map. Value of 1 represents the magitude on that vector is the local maximum. Thus, when calculating fiber tracks, it should be considered one of the possible orientations of the fiber track on that voxel. MAX file consists of 2 byte short integers.