update user docs to reflect recent changes

docs/reference/commands/dwinormalise.rst

@@ -22,7 +22,7 @@ Intensity normalise the b=0 signal within a supplied white matter mask
 Options
 -------
 
--  **-intensity value** normalise the b=0 signal to the specified value (Default: 1e+03)
+-  **-intensity value** normalise the b=0 signal to the specified value (Default: 1e+003)
 
 -  **-percentile value** define the percentile of the mask intensties used for normalisation. If this option is not supplied then the median value (50th percentile) will be normalised to the desired intensity value.
 

docs/reference/commands/mrconvert.rst

@@ -31,6 +31,15 @@ Options
 
 -  **-scaling values** specify the data scaling parameters used to rescale the intensity values. These take the form of a comma-separated 2-vector of floating-point values, corresponding to offset & scale, with final intensity values being given by offset + scale * stored_value. By default, the values in the input image header are passed through to the output image header when writing to an integer image, and reset to 0,1 (no scaling) for floating-point and binary images. Note that his option has no effect for floating-point and binary images.
 
+Modify generic header entries
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+-  **-clear_property key** remove the specified key from the image header altogether.
+
+-  **-set_property key value** set the value of the specified key in the image header.
+
+-  **-append_property key value** append the given value to the specified key in the image header (this adds the value specified as a new line in the header value).
+
 Stride options
 ^^^^^^^^^^^^^^
 

docs/reference/commands/mrview.rst

@@ -114,6 +114,10 @@ Tractography tool options
 
 -  **-tractography.load tracks** Load the specified tracks file into the tractography tool.
 
+-  **-tractography.thickness value** Line thickness of tractography display, [-1.0, 1.0], default is 0.0.
+
+-  **-tractography.opacity value** Opacity of tractography display, [0.0, 1.0], default is 1.0.
+
 ODF tool options
 ^^^^^^^^^^^^^^^^
 

docs/reference/commands/tckconvert.rst

@@ -20,6 +20,12 @@ Convert between different track file formats.
 
 The program currently supports MRtrix .tck files (input/output), ascii text files (input/output), and VTK polydata files (output only).
 
+Note that ascii files will be stored with one streamline per numbered file. To support this, the command will use the multi-file numbering syntax, where square brackets denote the position of the numbering for the files, for example:
+
+$ tckconvert input.tck output-[].txt
+
+will produce files named output-0000.txt, output-0001.txt, output-0002.txt, ...
+
 Options
 -------
 

docs/reference/commands/tcksift2.rst

@@ -77,7 +77,7 @@ Options for controlling the SIFT2 optimisation algorithm
 
 -  **-max_coeff_step step** maximum change to a streamline's weighting coefficient in a single iteration (default: 1)
 
--  **-min_cf_decrease frac** minimum decrease in the cost function (as a fraction of the initial value) that must occur each iteration for the algorithm to continue (default: 2.5e-05)
+-  **-min_cf_decrease frac** minimum decrease in the cost function (as a fraction of the initial value) that must occur each iteration for the algorithm to continue (default: 2.5e-005)
 
 Standard options
 ^^^^^^^^^^^^^^^^

docs/reference/commands_list.rst

@@ -165,10 +165,10 @@ List of MRtrix3 commands
 
    commands/tcksample
 
-   commands/tcksift2
-
    commands/tcksift
 
+   commands/tcksift2
+
    commands/tckstats
 
    commands/tensor2metric