Here is a list of all files with brief descriptions:

[detail level 123456]

▼ core
► adapter
base.h
extract.h
gaussian1D.h
gradient1D.h
gradient3D.h
jacobian.h
median.h
neighbourhood3D.h
normalise3D.h
permute_axes.h
regrid.h
replicate.h
reslice.h
subset.h
warp.h
► algo
copy.h
histogram.h
iterator.h
loop.h
min_max.h
neighbourhooditerator.h
random_loop.h
random_threaded_loop.h
stochastic_threaded_loop.h
threaded_copy.h
threaded_loop.h
► dwi
gradient.h
shells.h
► eigen_plugins
array.h
dense_base.h
matrix.h
► file
► dicom
csa_entry.h
definitions.h
element.h
image.h
mapper.h
patient.h
quick_scan.h
series.h
study.h
tree.h
config.h
copy.h
entry.h
gz.h
json_utils.h
key_value.h
mmap.h
name_parser.h
nifti2.h
nifti_utils.h
ofstream.h
path.h
png.h
tiff.h
utils.h
► filter
base.h
connected_components.h
dilate.h
dwi_brain_mask.h
erode.h
fft.h
gradient.h
mask_clean.h
median.h
normalise.h
optimal_threshold.h
resize.h
reslice.h
smooth.h
warp.h
zclean.h
► fixel
► legacy
fixel_metric.h
image.h
keys.h
helpers.h
keys.h
loop.h
types.h
► formats
list.h
mrtrix_utils.h
► image_io
base.h
default.h
fetch_store.h
gz.h
mosaic.h
pipe.h
png.h
ram.h
scratch.h
sparse.h
tiff.h
variable_scaling.h
► interp
base.h
cubic.h
linear.h
masked.h
nearest.h
sinc.h
► math
► stats
fwe.h
glm.h
import.h
shuffle.h
typedefs.h
average_space.h
bessel.h
betainc.h
cauchy.h
chebyshev.h
check_gradient.h
condition_number.h
constrained_least_squares.h
cubic_spline.h
erfinv.h
factorial.h
gaussian.h
golden_section_search.h
gradient_descent.h
gradient_descent_bb.h
hermite.h
least_squares.h
legendre.h
math.h
median.h
polynomial.h
quadratic_line_search.h
rician.h
rng.h
sech.h
SH.h
sinc.h
Sn_scale_estimator.h
sphere.h
welch_satterthwaite.h
ZSH.h
zstatistic.h
► misc
bitset.h
voxel2vector.h
app.h
apply.h
axes.h
cmdline_option.h
command.h
datatype.h
debug.h
exception.h
header.h
image.h
image_diff.h
image_helpers.h
memory.h
mrtrix.h
ordered_thread_queue.h
phase_encoding.h
progressbar.h
raw.h
signal_handler.h
signals.h
stats.h
stride.h
thread.h
thread_queue.h
timer.h
transform.h
types.h
version.h
▼ src
► connectome
connectome.h
enhance.h
lut.h
mat2vec.h
► doc
examples
► dwi
► directions
file.h
mask.h
predefined.h
set.h
► sdeconv
csd.h
msmt_csd.h
► tractography
► ACT
act.h
gmwmi.h
method.h
shared.h
tissues.h
► algorithms
calibrator.h
fact.h
iFOD1.h
iFOD2.h
nulldist.h
sd_stream.h
seedtest.h
tensor_det.h
tensor_prob.h
► connectome
connectome.h
exemplar.h
extract.h
mapped_track.h
mapper.h
matrix.h
metric.h
streamline.h
tck2nodes.h
► editing
editing.h
loader.h
receiver.h
worker.h
► GT
energy.h
externalenergy.h
gt.h
internalenergy.h
mhsampler.h
particle.h
particlegrid.h
particlepool.h
spatiallock.h
► mapping
► gaussian
mapper.h
voxel.h
buffer_scratch_dump.h
fixel_td_map.h
loader.h
mapper.h
mapper_plugins.h
mapping.h
twi_stats.h
voxel.h
writer.h
► resampling
arc.h
downsampler.h
endpoints.h
fixed_num_points.h
fixed_step_size.h
resampling.h
upsampler.h
► seeding
base.h
basic.h
dynamic.h
gmwmi.h
list.h
seeding.h
► SIFT
fixel.h
gradient_sort.h
model.h
model_base.h
output.h
proc_mask.h
sift.h
sifter.h
track_contribution.h
track_index_range.h
types.h
► SIFT2
coeff_optimiser.h
fixel.h
fixel_updater.h
line_search.h
reg_calculator.h
regularisation.h
streamline_stats.h
tckfactor.h
► tracking
early_exit.h
exec.h
generated_track.h
method.h
shared.h
tractography.h
types.h
write_kernel.h
file.h
file_base.h
properties.h
rng.h
roi.h
scalar_file.h
streamline.h
weights.h
bootstrap.h
fixel_map.h
fmls.h
noise_estimator.h
tensor.h
► fixel
► filter
base.h
connect.h
smooth.h
index_remapper.h
matrix.h
► gui
► dialog
dialog.h
dicom.h
file.h
image_properties.h
list.h
opengl.h
progress.h
report_exception.h
► dwi
render_frame.h
renderer.h
► mrview
► mode
base.h
lightbox.h
lightbox_gui.h
list.h
ortho.h
slice.h
volume.h
► sync
client.h
enums.h
interprocesscommunicator.h
localsocketreader.h
processlock.h
syncmanager.h
► tool
► connectome
colourmap_observers.h
connectome.h
edge.h
file_data_vector.h
matrix_list.h
node.h
node_list.h
node_overlay.h
selection.h
shaders.h
types.h
► fixel
base_fixel.h
directory.h
fixel.h
image4D.h
legacy.h
vector_structs.h
► odf
item.h
model.h
odf.h
preview.h
type.h
► roi_editor
item.h
model.h
roi.h
undoentry.h
► tractography
track_scalar_file.h
tractogram.h
tractogram_enums.h
tractography.h
base.h
list.h
list_model_base.h
overlay.h
screen_capture.h
transform.h
view.h
adjust_button.h
colourbars.h
colourmap_button.h
colourmap_menu.h
combo_box_error.h
displayable.h
file_open.h
gui_image.h
icons.h
spin_box.h
volume.h
window.h
► opengl
font.h
gl.h
lighting.h
shader.h
transformation.h
► shapes
cube.h
cylinder.h
halfsphere.h
sphere.h
► shview
file_open.h
icons.h
render_window.h
color_button.h
crosshair.h
cursor.h
gui.h
lighting_dock.h
projection.h
► registration
► metric
cc_helper.h
cross_correlation.h
demons.h
demons4D.h
demons_cc.h
difference_robust.h
evaluate.h
linear_base.h
local_cross_correlation.h
mean_squared.h
params.h
robust_estimators.h
thread_kernel.h
► transform
affine.h
base.h
convergence_check.h
initialiser.h
initialiser_helpers.h
reorient.h
rigid.h
search.h
► warp
compose.h
convert.h
helpers.h
invert.h
linear.h
multi_contrast.h
multi_resolution_lmax.h
nonlinear.h
shared.h
► stats
cfe.h
cluster.h
enhance.h
permstack.h
permtest.h
tfce.h
► surface
► algo
image2mesh.h
mesh2image.h
► filter
base.h
smooth.h
vertex_transform.h
freesurfer.h
mesh.h
mesh_multi.h
polygon.h
scalar.h
types.h
utils.h
colourmap.h
exec_version.h
min_mem_array.h
wrap_r.h