diff --git a/docs/reference/commands/afdconnectivity.rst b/docs/reference/commands/afdconnectivity.rst index c356e6ad7b..10c2088e18 100644 --- a/docs/reference/commands/afdconnectivity.rst +++ b/docs/reference/commands/afdconnectivity.rst @@ -31,7 +31,7 @@ For valid comparisons of AFD connectivity across scans, images MUST be intensity Note that the sum of the AFD is normalised by streamline length to account for subject differences in fibre bundle length. This normalisation results in a measure that is more related to the cross-sectional volume of the tract (and therefore 'connectivity'). Note that SIFT-ed tract count is a superior measure because it is unaffected by tangential yet unrelated fibres. However, AFD connectivity may be used as a substitute when Anatomically Constrained Tractography is not possible due to uncorrectable EPI distortions, and SIFT may therefore not be as effective. -Longer discussion regarding this command can additionally be found at: https://mrtrix.readthedocs.io/en/3.0.2/concepts/afd_connectivity.html (as well as in the relevant reference). +Longer discussion regarding this command can additionally be found at: https://mrtrix.readthedocs.io/en/3.0.3/concepts/afd_connectivity.html (as well as in the relevant reference). Options ------- diff --git a/docs/reference/commands/amp2sh.rst b/docs/reference/commands/amp2sh.rst index 7621f80c2d..3cde09ed9d 100644 --- a/docs/reference/commands/amp2sh.rst +++ b/docs/reference/commands/amp2sh.rst @@ -26,7 +26,7 @@ The spherical harmonic decomposition is calculated by least-squares linear fitti The directions can be defined either as a DW gradient scheme (for example to compute the SH representation of the DW signal), a set of [az el] pairs as output by the dirgen command, or a set of [ x y z ] directions in Cartesian coordinates. The DW gradient scheme or direction set can be supplied within the input image header or using the -gradient or -directions option. Note that if a direction set and DW gradient scheme can be found, the direction set will be used by default. The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link: |br| -https://mrtrix.readthedocs.io/en/3.0.2/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.3/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/dwi2fod.rst b/docs/reference/commands/dwi2fod.rst index 4c78bc24e3..6ee58804b5 100644 --- a/docs/reference/commands/dwi2fod.rst +++ b/docs/reference/commands/dwi2fod.rst @@ -23,7 +23,7 @@ Description ----------- The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link: |br| -https://mrtrix.readthedocs.io/en/3.0.2/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.3/concepts/spherical_harmonics.html Example usages -------------- diff --git a/docs/reference/commands/fixel2sh.rst b/docs/reference/commands/fixel2sh.rst index 3889489c1c..4d9901fac6 100644 --- a/docs/reference/commands/fixel2sh.rst +++ b/docs/reference/commands/fixel2sh.rst @@ -24,7 +24,7 @@ Description This command generates spherical harmonic data from fixels that can be visualised using the ODF tool in MRview. The output ODF lobes are scaled according to the values in the input fixel image. The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link: |br| -https://mrtrix.readthedocs.io/en/3.0.2/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.3/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/sh2amp.rst b/docs/reference/commands/sh2amp.rst index 91d78ba6a5..c43e1fa6c1 100644 --- a/docs/reference/commands/sh2amp.rst +++ b/docs/reference/commands/sh2amp.rst @@ -35,7 +35,7 @@ If a full DW encoding is provided, the number of shells needs to match those fou If the input image contains multiple shells (its size along the 5th dimension is greater than one), the program will expect the direction set to contain multiple shells, which can only be provided as a full DW encodings (the last two options in the list above). The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link: |br| -https://mrtrix.readthedocs.io/en/3.0.2/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.3/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/sh2peaks.rst b/docs/reference/commands/sh2peaks.rst index 86c59cbe39..d117781b35 100644 --- a/docs/reference/commands/sh2peaks.rst +++ b/docs/reference/commands/sh2peaks.rst @@ -24,7 +24,7 @@ Description Peaks of the spherical harmonic function in each voxel are located by commencing a Newton search along each of a set of pre-specified directions The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link: |br| -https://mrtrix.readthedocs.io/en/3.0.2/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.3/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/sh2power.rst b/docs/reference/commands/sh2power.rst index 507a0b1c79..3b0fc40654 100644 --- a/docs/reference/commands/sh2power.rst +++ b/docs/reference/commands/sh2power.rst @@ -24,7 +24,7 @@ Description This command computes the sum of squared SH coefficients, which equals the mean-squared amplitude of the spherical function it represents. The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link: |br| -https://mrtrix.readthedocs.io/en/3.0.2/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.3/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/sh2response.rst b/docs/reference/commands/sh2response.rst index 22cbcc90fa..f58863576f 100644 --- a/docs/reference/commands/sh2response.rst +++ b/docs/reference/commands/sh2response.rst @@ -24,7 +24,7 @@ Description ----------- The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link: |br| -https://mrtrix.readthedocs.io/en/3.0.2/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.3/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/shbasis.rst b/docs/reference/commands/shbasis.rst index bc1dc94e47..fd396b3181 100644 --- a/docs/reference/commands/shbasis.rst +++ b/docs/reference/commands/shbasis.rst @@ -27,7 +27,7 @@ This command provides a mechanism for testing the basis used in storage of image Note that the "force_*" conversion choices should only be used in cases where this command has previously been unable to automatically determine the SH basis from the image data, but the user themselves are confident of the SH basis of the data. The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link: |br| -https://mrtrix.readthedocs.io/en/3.0.2/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.3/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/shconv.rst b/docs/reference/commands/shconv.rst index 6acae630d1..2b2fd14ed7 100644 --- a/docs/reference/commands/shconv.rst +++ b/docs/reference/commands/shconv.rst @@ -28,10 +28,10 @@ If multiple pairs of inputs are provided, their contributions will be summed int If the responses are multi-shell (with one line of coefficients per shell), the output will be a 5-dimensional image, with the SH coefficients of the signal in each shell stored at different indices along the 5th dimension. The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link: |br| -https://mrtrix.readthedocs.io/en/3.0.2/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.3/concepts/spherical_harmonics.html The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link: |br| -https://mrtrix.readthedocs.io/en/3.0.2/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.3/concepts/spherical_harmonics.html Options -------