Paul's Software
The programs are grouped in general sections, however there is considerable
cross-functionality between several projects, particularly the programs with
graphical user interfaces. Many programs, especially those converting between
image formats, call other programs in the background. To allow this to happen
it is best to include Paul's bin directory in your PATH environment
variable.
All programs will compile and run under UNIX or GNU/Linux. The graphical
programs require the Openwindows/xview libraries. Most of the
non-GUI software can be compiled using a 32-bit Windows compiler to run in a
command window in
Microsoft
Windows, while the graphical programs may be compiled
to run under Windows using
Cygwin
in combination with the
xview toolkit compiled for Cygwin.
Also see
environment variable settings for xview.
The source code is not available for general download. However, for
collaborators who do have the source code, there are a few
notes on how to compile it.
Image Browser for X Windows
- ibx (GUI)
- Graphical viewer to display a range of medical image formats.
Conversion
- dtoa
- Converts a subdirectory structure of DICOM images to ACR/NEMA and Analyze/NIFTI
format globally, sorting images by patient ID. Also contains options to run
subsequent post-processing scripts on relevant converted images, e.g.,
further processing of diffusion-weighted images to create FA maps.
- acrtoana
- Converts DICOM and ACR/NEMA image format to Analyze or NIFTI format, within
a single subdirectory and without sorting the source images.
- ptoa
- Converts Philips PAR/REC image format to Analyze or NIFTI format.
- sortspec
- Sorts exported raw spectroscopy data from GE, Philips, and Siemens MR
scanners into a pre-defined directory structure.
- ntoa
- Converts NIFTI files to Analyze format.
Manipulation
- mirrot
- Performs simple mirroring, rotation, and scrolling on Analyze images.
- swap34
- Reorders multi-volume Analyze images by swapping the 3rd and
4th dimensions.
- swapana
- Swaps byte order in Analyze image and header file to convert between
little-endian and big-endian.
- interleave
- Combines two or more Analyze file to produce a single interleaved Analyze
file.
- mergestacks
- Takes an Analyze file containing more than one stack (overlapping volume)
and produces a file in which the overlapping slices have been merged together.
- mp2rage
- Calculates the MP2RAGE image from the modulus and phase data from a
MR scan acquired at two inversion times following a single inversion pulse.
- swi
- Susceptibility Weighted Imaging post-processing. Takes Analyze files
containing T2* weighted images (modulus and phase) and calculates the
SWI.
- syncphysio
- Synchronises log files of physiological recordings made by the MR scanner to
the time of image acquisition as stored in the DICOM files.
Perfusion Analysis
- perf (GUI)
- Produces perfusion parameters from T1 or T2* weighted
images acquired during injection of a bolus of paramagnetic contrast agent.
Also performs basic ASL analysis.
Relaxometry
- irt1map
- Calculates a T1 map from several modulus inversion recovery
images acquired with different inversion times.
- t2map
- Calculates a T2 map from several images acquired with different
echo times.
- wme
- Calculates a mean image from a dynamic multi-echo acquisition
(e.g., a dual-echo fMRI acquisition) weighted by the T2
pixel values.
General
- comqa
- Performs simple statistics and tracking of the centre of mass of a phantom
to assess drifts and trends for a typical multivolume fMRI acquisition.