Slightly faster SH basis implementation by eliminating unnecessary sines and cosines.
DWI::SDeconv: support direct response function input as vector of coefs

Allows the response function coefficients to be provided as a list of
comma-separated values, or as a file. The application will try to parse
the list as a vector a values first, and load the file if that fails.
DWI::Shells: update to option documentation
Fix compilation warning due to returning NAN instead of int
New command 'warpinit'

Provides replacement for 0.2 'gen_unit_warp' command.
removed incomplete registration code
removed some unnecessary code
Carry scaling factors through copy construction for Image::ConstHeader

Since the Image::Buffer classes derive from ConstHeader, this should
ensure that the scaling factors specified in the original header are
properly accounted for in the output image. This relates to issue #2.
Image::BufferPreload now also perform pre-load if scaling factors are not (0,1)

This is important since the scaling factors are not applied when
retrieving image intensity values, in contrast to the Image::Buffer
class.
Merge pull request #1 from jdtournier/sh_basis

Slightly faster SH basis implementation.
tckgen: use enum names for track termination & rejection
tckgen seeding classes: move virtual methods to cpp file
Seeding::Default renamed to Seeding::SeedMask
tckgen: changes to sampling strategy at the seed point

As discussed in issue #33, the continous search (by rejection sampling)
for a suitable start direction at the seed point causes slowdowns for
iFOD1 & iFOD2 since the maximum number of trials is 1000 by default,
which causes the algorithm to spend a lot of time sampling at unsuitable
seed locations before trying a different seed location. These changes
make sure the algorithm only tries one direction per seed location when
using an unlimited number of seed points, while ensuring that seeding
strategies with a fixed number of seed point (e.g. -seed_grid_per_voxel,
-seed_random_per_voxel) still try hard to initiate a track from each
seed point.
added qtcreator project files to git ignore - bye bye eclipse you slow old dog
Changed seeding threshold to be equal to tracking threshold

Previously, the default FA/FOD amplitude threshold when finding a seed point was twice the threshold used during streamline propagation.
This has now been changed to be equivalent to the tracking threshold.
This was deemed to be more appropriate given recent changes to how the seeding is performed.
Variable maximum number of tracking attempts from seed point

As discussed in Issue #41.
Once an appropriate seed point is determined, a probabilistic tracking algorithm may take some number of attempts to find a suitable direction to commence tracking.
The maximum number of attempts now depends on the mechanism used to generate the seed points.
For instance, if the seed points are drawn randomly from a mask image, only 1 direction is tested per seed point; whereas if seeds are defined on a lattice grid, every attempt is made to find a valid tracking direction from every seed point.
This behaviour can be overridden using the -max_seed_attempts option.
Fixes to revpe_distcorr script

Fixes issue #44.
Script will now accept reverse phase-encode input images that have a trailing unary axis.
Also fixed error in automatic cropping of input images with non-even spatial axis dimensions.
Added -stop option to tckgen

Closes #40.
Just as in MRtrix 0.2, the new -stop option instructs the tractography algorithm to cease streamline propagation as soon as a given streamline has entered all inclusion regions.
A warning will be produced if the user tries to apply this option but does not provide any inclusion regions.
This option cannot be used in conjunction with back-tracking in ACT.
Small fix to SIFT debugging image output