From Camino

Man: Pdview

Content-type: text/html Manpage of pdview


Section: User Commands (1)
Index Return to Main Contents


pdview - Visualizes principal direction(s) in each voxel



pdview -inputmodel <dteig (default) | pds | pico | ballstick> -datadims <x> <y> <z> [-scalarthresh <threshold>] [-scalarrange <min> <max>] [-scalarfile <file>] -norgb -maxcomponents <max tensors per voxel> | -numpds <max peaks per voxel>



This program displays the principal directions of diffusion tensors or the peak directions of spherical functions. The directions are overlaid on a scalar volume, which can be computed from the data or loaded from a file.

For tensor data, the program reads the eigen decomposition of a diffusion tensor volume, in the format produced by dteig. One or two tensors per voxel may be displayed. If there are more than two tensors in a voxel, only the first two PDs are displayed. The default scalar background is fractional anisotropy of the tensor (or the mean of the two tensors if there are two within the voxel).

For spherical function data, the program reads the output of sfpeaks. If there are more than two peaks in a voxel, only the first two PDs are displayed. The default scalar background is the trace of the Hessian of the first peak.

For PICo data, the program reads the output of picopdfs. The default scalar background is the sum of the absolute value of the concentration parameters in the voxel. The default number of PDFs per voxel is one, a maximum of two may be displayed. The default PDF is "bingham".

For ballstick data, the program reads the output of fanninggrid.

The scalar volume can be loaded from a file using the -scalarfile option. The scalar values should be positive, and of the same data type as the input data. The scalar values are mapped to grey levels according to the range of the data. The contrast range can be modified with the -scalarrange option.

The image is colored by the orientation of the PDs, or the mean orientation of the first two PDs in multi-fibre voxels. Turn off colors with -norgb.

The default plane view is axial and the user may switch to sagittal or coronal by clicking the buttons at the top of the screen. Next to the plane selection buttons is the currently selected slice, with the zoomed area outlined in yellow. Click anywhere on this image to centre the zoomed area. The main window shows the zoomed area in larger detail. The principal directions in each voxel are drawn as lines.

The default input data type is double.

This program can be used to edit scheme files. To use this function you must specify the the scheme file you wish to edit using the -schemefile flag. This will enable the scheme file editor buttons. Although the controls allow you to edit your schemefile, they do not update the corresponding PDs (or diffusion tensors). If you modify a scheme file, you will need to recalculate the PDs or diffusion tensors for the changes to take effect.



Run dteig on a 128x128x60 tensor data set, and view the principal directions.

dteig < subjectA.inv1.Bdouble | pdview -datadims 128 128 60 -inputmodel dteig

Read data from the file subjectA.Inv1.eig.Bdouble and display principal directions in white matter.

pdview -inputfile subjectA.Inv1.eig.Bdouble -datadims 128 128 60 -scalarthresh 0.15 -inputmodel dteig

Display principal directions for a multi-tensor volume (see multitenfit(1)).

dteig -inputmodel multitensor < subjectA.Inv32.Bdouble | pdview -datadims 128 128 60 -maxcomponents 2 -inputmodel dteig

Display output of sfpeaks, but use a tensor FA map as scalar background.

fa < subjectA.Inv1.Bdouble > subjectA.fa.Bdouble

pdview -datadims 128 128 60 -inputmodel pds -scalarfile subjectA.fa.Bdouble < subjectA.sfpeaks.Bdouble

Show Watson PICo pdfs

picopdfs -pdf watson -luts watsonLUT -inputfile subjectA.inv1.Bdouble > watsonPDFs.Bdouble

pdview -inputmodel pico -pdf watson -datadims 128 128 60 < watsonPDFs.Bdouble



-datadims <x> <y> <z>
The dimensions of the image, in voxels.

-voxeldims <x> <y> <z>
The x, y, and z dimension of each voxel, in millimetres. Not needed for display, but necessary to correctly save the RGB data.

-inputmodel <model>
Either "dteig" (tensor eigensystems, default), "pds" (spherical function peaks), "pico" (PICo PDFs) or "ballstick" (ball and stick partial volume model).

-scalarfile <file>
Specifies the scalar imaged used as the greyscale image. Either an Analyze / ITK / NIFTI-1 image or a raw binary data file. If a header is specified, the -datadims and -voxeldims arguments are not necessary and are ignored.

If a binary file is specified, then the data type should be the same as the input data, which is double unless otherwise specified with the (-inputdatatype) option.

Whichever kind of scalar file is used, it should be defined in the same space as the diffusion data.

If no scalar file is given, the default background depends on the input model.

   dteig        fractional anisotropy
   pds          hessian trace
   pico         modulus of the mean concentration parameter
   ballstick    anisotropic mixing fraction

-scalarrange <min> <max>
The minimum and maximum range of scalar values to display as different grey levels. Any voxels below the min will be black, those above the max will be white. By default, this range is calculated from the data (the smallest and largest 0.5% of scalars are excluded from the calculation so that outliers do not reduce the contrast).

-scalarthresh <value>
The scalar threshold. The principal direction is not displayed in a voxel unless the associated scalar is greater than the specified value. Must be greater than or equal to the minimum scalar value specified with -scalarrange. The default is 0.

-maxcomponents <max tensors per voxel>
Maximum number of tensor components in each voxel, for dteig data. The default is 1.

-numpds <max PDs per voxel>
Maximum number of spherical function peaks in each voxel, for pd data, PICo data and ballstick data. The default is 3 for pd data and 1 for the others.

-pdf <bingham | watson | acg>
PDF type of PICo data. The default is "bingham".

The default behaviour is to colour the scalar image by the components of the PD (X->R, Y->G, Z->B). Use this option to display a grayscale image.

Used only for tensor or pico data. Uses the first eigenvector to construct the RGB image,
 corresponding to the largest eigenvalue of the tensor. This is the default.

Used only for tensor or pico data. Uses the second eigenvector to construct the RGB image.

Used only for tensor or pico data. Uses the third eigenvector to construct the RGB image,
 corresponding to the smallest eigenvalue of the tensor.

-schemefile <Scheme file name>
See modelfit(1).



Philip Cook, Kiran Seunarine <>



dteig(1), sfpeaks(1)






This document was created by man2html, using the manual pages.
Time: 02:07:11 GMT, December 04, 2017

Retrieved from
Page last modified on October 26, 2009, at 02:58 PM