This produces a tensor volume in which the tensors are rotated 180 degrees about the x axis.
 
 
ADD A PARAGRAPH ABOUT -TRANS OPTION
 

TVtool -in tensor.nii.gz -reorient -euler 180 -out reoriented.nii.gz

DTI-TK implements the utilities to compute the common rotation-invariant scalar indices derived from a DTI volume.  The scalar index volumes are saved in NIfTI format and can be visualized using any Analyze/NIfTI supported viewers, such as [[http://www.cabiatl.com/mricro/| MRIcro]] and [[http://www.itksnap.org/pmwiki/pmwiki.php|ITK-SNAP]].  The utilities to compute rotation-invariant scalar indices are described [[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.TVtool|here]].
 

%lframe height=250%Attach:axial_tensor.png %height=250%Attach:coronal_tensor.png
 
 

To correct for any errors that you identify, you need to first modify the gradient table, then repeat the tensor reconstruction.  The modification of the gradient table typically involves flipping the signs of the x or y component of all gradient vectors.  To determine the correct flipping of the signs in a systematic way, it is necessary to understand why this happens.  The reason is that the gradient directions are always defined with respect to some right-handed frame of reference, while the frame of reference of the acquired image data is typically NOT right-handed. This mismatch is the cause of the problem.  The sign flipping intends to fix this mismatch and the key is to identify the difference between the two frames of reference in question. In our experience, if the data is acquired on SIEMENS scanners, the signs of x gradient components need to be flipped; for GE scanners, it is usually the y components.
 
In the event that you prefer not to redo the tensor reconstruction, you can correct the tensor orientations with the tool TVReorient, which allows you to specify the appropriate rotation, in terms of Euler angles, that should be applied to each tensor in the volume. The Euler angles are theta, the rotation about x axis, phi, the rotation about y axis, and psi, the rotation about z axis.  The sign flipping of x component is equivalent to setting theta to 180 degrees, phi and psi to 0 degrees.  Similarly, the flipping of y component is equivalent to setting phi to 180 degrees, theta and psi to 0 degrees.  Here is an example usage:
 
->[@TVReorient -in input.nii.gz -theta 180 -out reoriented.nii.gz

#Using the most recent version of MRIcron, you can load a DTI volume in NIfTI format directly.  The program will prompt you to pick the tensor component that you'd like to view.

 

The figures below illustrate the axial and coronal views produced for the example data.
 
%lframe height=200%Attach:axial_tensor.png %height=200%Attach:coronal_tensor.png
 
 

%lframe width=300%Attach:axial_tensor.png Attach:coronal_tensor.png
 
 

%lframe width=300%Attach:axial_tensor.png
%rframe width=300%Attach:coronal_tensor.png
 

%lframe width=500%Attach:axial_tensor.png
%rframe width=500%Attach:coronal_tensor.png
 

'a'|'A': rotate out-of-plane 5 degrees counterclockwise|clockwise
'f'|'F': increase|decrease ellipsoid scaling factor
'r': reset to original view
's'|'S': rotate in-plane 5 degrees counterclockwise|clockwise
'x': flip left and right
'y': flip up and down
','|'.': go to the slice below|above
'j'|'k': shift the view to left|right
'h'|'l': shift the view up|down
'p': save the current rendering in a png file
'1': toggle the visibility of the tensor glyphs
'2': toggle the visibility of the background or overlay if supplied
'3': toggle the visibility of the outline
'4': toggle the visibility of the red arrow
'5': toggle the visibility of the green arrow
'6': toggle the visibility of the blue arrow
 
 

In order to adjust the visualization of your image, here is another list for the complete usage of TVglyphView
 

 
 
 
**********
first determine the dimensions of the volume, if not yet done.  You can use the command
 

(:cell align=center:) COAS Specify the type of glyph rendering: color orientation (CO), anisotropy scaling (AS), color orientation and anisotropy scaling (COAS), original (OR)

(:cell align=center:) axial Specify the slice view: axial, sagittal, or coronal, default to axial

(:cell align=center:) If not specified, will use the center of the volume (in voxel unit)

(:cell align=center:) If not specified, will use the maximum size

(:cell align=center:) axial 
(:cell align=center:) Specify the slice view: axial, sagittal, or coronal, default to axial

(:cell align=center:) N

[[http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.TVtool|TVtool]] can be used to compute the principal diffusion direction map of a DTI volume or to map the principal diffusion direction into the corresponding RGB map, which can be visualized using ITK-SNAP. 
 

outputs the RGB map ''tensor_rgb.nii.g'' that can be directly loaded into ITK-SNAP for viewing.  The script also allows for an additional parameter to tune the saturation level of colors.  If not supplied, the default value is 1.0.  The command
 

DTI-TK implements tools for visualizing the tensors in terms of 3D ellipsoid glyphs and these tools are aimed to remedy the shortcomings of RGB-based visualization discussed above.  To visualize a DTI volume, first determine the dimensions of the volume, if not yet done.  You can use the command
 
->[@ VolumeInfo tensor.nii.gz

%width=100%Attach:rgb_image.png
 
 

%width=10cm%Attach:rgb_image.png
 
 

Attach:rgb_image.png
 
 

 
 

! Visualizing DTI images with DTI-TK
 

Effective visualization of DTI volumes is critically important for processing and analyzing this type of data.  For example, after reconstructing a DTI volume from the raw diffusion-weighted images (DWIs), it is imperative to examine if the tensors are properly oriented in space.  For this purpose, neither the FA map nor the RGB map of the principal diffusion directions suffice.  It is necessary to visualize the principal diffusion direction as 3D vectors or to visualize the tensors as 3D tensor glyphs.  DTI-TK offers a simple tool for the latter.
 

%width=400px% Attach:rgb_image.png
 
 

 

 DTI-TK implements tools for visualizing the tensors in terms of 3D ellipsoid glyphs and these tools are aimed to remedy the shortcomings of RGB-based visualization discussed above.  To visualize a DTI volume, first determine the dimensions of the volume, if not yet done.  You can use the command
 

The last number adjusts the scaling of the ellipsoid sizes, while the other integers specify a bounding box, or a bounding slice to be more precise.  The first two integers specify the range of x slices, the middle two the range of y slices, and the last two the range of z slices.  Note that the slices are indexed beginning from 0.  By setting the two integers for the z slices to be identical, the program is instructed to show an axial slice.  Similarly, the following command will show a coronal slice through the volume (the coronal slice 56)
 

The ellipsoidImageColOriAniScl has a number of useful functionalities which are accessed via keystroke controls.  Hit the key 'H' will print out the complete list of keyboard controls.  The list includes:

    List of the available keystroke controls
    'H': print this keystroke control list
   'a'|'A': rotate out-of-plane 5 degrees counterclockwise|clockwise
  'f'|'F': increase|decrease ellipsoid scaling factor
    'r': reset to original view
   's'|'S': rotate in-plane 5 degrees counterclockwise|clockwise
   'x': flip left and right
    'y': flip up and down
    ','|'.': go to the slice below|above
    'j'|'k': shift the view to left|right
    'h'|'l': shift the view up|down
    'p': save the current rendering in a png file
    '1': toggle the visibility of the tensor glyphs
    '2': toggle the visibility of the background or overlay if supplied
    '3': toggle the visibility of the outline
    '4': toggle the visibility of the red arrow
    '5': toggle the visibility of the green arrow
    '6': toggle the visibility of the blue arrow
 

 
An important utility of the tensor glyph rendering described above is for checking the correctness of your tensor reconstruction.  A common mistake during tensor reconstruction (the process of constructing tensor volumes from diffusion-weighted images) is using a gradient table that is not corrected for the difference between the coordinate frame in which the gradient table is defined and the one in which the image is defined.  This type of erroneous reconstruction can not be detected with the RGB map (explained above) and need to be ruled out with the tensor glyph rendering.
 

To correct for any errors that you identify, you need to first modify the gradient table, then repeat the tensor reconstruction.  The modification of the gradient table typically involves flipping the signs of the x or y component of all gradient vectors.  To determine the correct flipping of the signs in a systematic way, it is necessary to understand why this happens.  The reason is that the gradient directions are always defined with respect to some right-handed frame of reference, while the frame of reference of the acquired image data is typically NOT right-handed.  This mismatch is the cause of the problem.  The sign flipping intends to fix this mismatch and the key is to identify the difference between the two frames of reference in question.  In our experience, if the data is acquired on SIEMENS scanners, the signs of x gradient components need to be flipped; for GE scanners, it is usually the y components.
 
In the event that you prefer not to redo the tensor reconstruction, you can correct the tensor orientations with the tool TVReorient, which allows you to specify the appropriate rotation, in terms of Euler angles, that should be applied to each tensor in the volume.
The Euler angles are theta, the rotation about x axis, phi, the rotation about y axis, and psi, the rotation about z axis.  The sign flipping of x component is equivalent to setting theta to 180 degrees, phi and psi to 0 degrees.  Similarly, the flipping of y component is equivalent to setting phi to 180 degrees, theta and psi to 0 degrees.  Here is an example usage:
 

 
# Using TensorVolumeToImage, you can split a DTI volume in NIfTI format into six scalar NIfTI volumes.  Each scalar volume contains one of the six tensor components and can be viewed with standard volume viewers, such as ITK-SNAP.  Below is an example usage of TensorVolumeToImage applied to the provided sample data.
 

# Using the most recent version of MRIcron, you can load a DTI volume in NIfTI format directly.  The program will prompt you to pick the tensor component that you'd like to view.

    $ VolumeInfo tensor.nii.gz
 

    Volume Info of tensor.nii.gz
    size: 112x112x60, voxel size: 2x2x2, origin: [0, 0, 0]
 

    $ ellipsoidImageColOriAniScl tensor.nii.gz 0 111 0 111 29 29 1.0
 

    $ ellipsoidImageColOriAniScl tensor.nii.gz 0 111 55 55 0 59 1.0
 

!! Checking if tensors are correctly reconstructed
 

    $ TVReorient -in input.nii.gz -theta 180 -out reoriented.nii.gz
 
!! Viewing the tensor component images
 

    $ TensorVolumeToImage tensor.nii.gz tensor nii.gz
 

%lframe width=400px% Attach:rgb_image.png
 
 

5. Checking if tensors are correctly reconstructed
 

1) Check if the tensors are oriented correctly in the genu and the splenium of the corpus callosum in the axial view (shown above).  The tensors' major axes should be clearly aligned along the boundary of the genu and the splenium.
 
2) Check if the tensors are oriented correctly in the internal capsule and the midbody of the corpus callosum in the coronal view (also shown above).  Again, the tensors should be properly aligned with the boundary of these structures.
 

6. Viewing the tensor component images
 

1) Using TensorVolumeToImage, you can split a DTI volume in NIfTI format into six scalar NIfTI volumes.  Each scalar volume contains one of the six tensor components and can be viewed with standard volume viewers, such as ITK-SNAP.  Below is an example usage of TensorVolumeToImage applied to the provided sample data.
 

2) Using the most recent version of MRIcron, you can load a DTI volume in NIfTI format directly.  The program will prompt you to pick the tensor component that you'd like to view.

%rframe width=50px% Attach:rgb_image.png
 
 

%rframe% Attach:rgb_image.png
 
 

%rframe% Attach:ellipsoid_axial.png
 
 

4. Viewing the tensors using 3D ellipsoid glyphs

%lframe% Attach: rgb_image.png
 
 

%lframe% Attach:rgb_image.tiff
 
 

1. Overview

Effective visualization of DTI volumes is critically important for processing and analyzing this type of data.  For example, after reconstructing a DTI volume from the raw diffusion-weighted images (DWIs), it is imperative to examine if the tensors are properly oriented in space.  For this purpose, neither the FA map and the RGB map of the principal diffusion directions suffice.  It is necessary to visualize the principal diffusion direction as 3D vectors or to visualize the tensors as 3D tensor glyphs.  DTI-TK offers a simple tool for the latter.
 

2. Viewing the rotation-invariant scalar indices 
 
DTI-TK implements the utilities to compute the common rotation-invariant scalar indices derived from a DTI volume.  The scalar index volumes are saved in NIfTI format and can be visualized using any Analyze/NIfTI supported viewers, such as MRIcro and ITK-SNAP.  The utilities to compute rotation-invariant scalar indices are described here .
 
3. Viewing the RGB map of the principal diffusion directions
 
DTI-TK implements a utility to compute the principal diffusion direction map of a DTI volume and another utility for mapping the principal diffusion direction map into the corresponding RGB map that can be visualized using ITK-SNAP.  The two utilities have been wrapped into a single bash script "pdrgb".  The following command
 
    $ pdrgb tensor.nii.gz

will output a RGB map "tensor_pd.mha" that can be directly loaded into ITK-SNAP for viewing.  The script also allows for an additional parameter to tune the saturation level of colors.  If not supplied, the default value is 1.0.  The command
 
    $ pdrgb tensor.nii.gz 1.5