From 32d17043ec75babbaed65b31d62c063b85ddfa24 Mon Sep 17 00:00:00 2001 From: J-Donald Tournier Date: Wed, 14 Dec 2022 09:57:27 +0000 Subject: [PATCH] updated documentation to match version change --- Dockerfile | 2 +- Singularity | 2 +- core/version.h | 2 +- docs/reference/commands/afdconnectivity.rst | 2 +- docs/reference/commands/amp2sh.rst | 2 +- docs/reference/commands/dwi2fod.rst | 2 +- docs/reference/commands/fixel2sh.rst | 2 +- docs/reference/commands/sh2amp.rst | 2 +- docs/reference/commands/sh2peaks.rst | 2 +- docs/reference/commands/sh2power.rst | 2 +- docs/reference/commands/sh2response.rst | 2 +- docs/reference/commands/shbasis.rst | 2 +- docs/reference/commands/shconv.rst | 4 ++-- 13 files changed, 14 insertions(+), 14 deletions(-) diff --git a/Dockerfile b/Dockerfile index 0a30e90d9f..ca7090a27f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,7 +7,7 @@ FROM buildpack-deps:buster AS base-builder FROM base-builder AS mrtrix3-builder # Git commitish from which to build MRtrix3. -ARG MRTRIX3_GIT_COMMITISH="master" +ARG MRTRIX3_GIT_COMMITISH="3.0.4" # Command-line arguments for `./configure` ARG MRTRIX3_CONFIGURE_FLAGS="" # Command-line arguments for `./build` diff --git a/Singularity b/Singularity index 21904e74fa..e7bf57d1fd 100644 --- a/Singularity +++ b/Singularity @@ -58,7 +58,7 @@ Include: apt ln -s /usr/bin/python3 /usr/bin/python # MRtrix3 setup - git clone -b master --depth 1 https://github.com/MRtrix3/mrtrix3.git /opt/mrtrix3 + git clone -b 3.0.4 --depth 1 https://github.com/MRtrix3/mrtrix3.git /opt/mrtrix3 cd /opt/mrtrix3 && ./configure && ./build -persistent -nopaginate && rm -rf testing/ tmp/ && cd ../../ # apt cleanup to recover as much space as possible diff --git a/core/version.h b/core/version.h index 4979d98509..4a1f7c1f9a 100644 --- a/core/version.h +++ b/core/version.h @@ -9,7 +9,7 @@ // git tag -s 3.3.0 // git push --follow-tags -#define MRTRIX_BASE_VERSION "3.0.3" +#define MRTRIX_BASE_VERSION "3.0.4" #endif diff --git a/docs/reference/commands/afdconnectivity.rst b/docs/reference/commands/afdconnectivity.rst index c9d2b8f3ab..46dbef7e29 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/3.0.3/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/3.0.4/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 d3cc0c8ce8..de34d2ae47 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/3.0.3/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/dwi2fod.rst b/docs/reference/commands/dwi2fod.rst index 5483d2e9d9..20221d204e 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/3.0.3/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html Example usages -------------- diff --git a/docs/reference/commands/fixel2sh.rst b/docs/reference/commands/fixel2sh.rst index 0f91668ef6..e929935bd9 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/3.0.3/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/sh2amp.rst b/docs/reference/commands/sh2amp.rst index 6207fd6ce5..ec50af75a0 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/3.0.3/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/sh2peaks.rst b/docs/reference/commands/sh2peaks.rst index fe3b766fd7..67f663f9ed 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/3.0.3/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/sh2power.rst b/docs/reference/commands/sh2power.rst index f6a9d38039..28b87dba4f 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/3.0.3/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/sh2response.rst b/docs/reference/commands/sh2response.rst index 873219496a..e7fff1dd13 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/3.0.3/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/shbasis.rst b/docs/reference/commands/shbasis.rst index 127dbe9097..9ac9314982 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/3.0.3/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/shconv.rst b/docs/reference/commands/shconv.rst index 240a23c42b..e23af61f6f 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/3.0.3/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.4/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/3.0.3/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html Options -------