diff --git a/Dockerfile b/Dockerfile index 8ba036b7a3..371daa4b09 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,7 +7,7 @@ FROM buildpack-deps:bookworm 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="3.0.8" # Command-line arguments for `./configure` ARG MRTRIX3_CONFIGURE_FLAGS="" # Command-line arguments for `./build` diff --git a/Singularity b/Singularity index b17eb16b1b..bd65c178f7 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 3.0.8 --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 669d2e24e0..2b23729497 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 "3.0.7" +#define MRTRIX_BASE_VERSION "3.0.8" #endif diff --git a/docs/reference/commands/afdconnectivity.rst b/docs/reference/commands/afdconnectivity.rst index 306d8f9a39..1bfc9400a0 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/3.0.7/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/3.0.8/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 9ec664a155..94ed36dbf2 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/3.0.7/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.8/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/dwi2fod.rst b/docs/reference/commands/dwi2fod.rst index 284b6a281e..2a798911ec 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/3.0.7/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.8/concepts/spherical_harmonics.html Example usages -------------- diff --git a/docs/reference/commands/fixel2sh.rst b/docs/reference/commands/fixel2sh.rst index 10d503bfca..18a1fd0c8c 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/3.0.7/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.8/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/sh2amp.rst b/docs/reference/commands/sh2amp.rst index 54c8bb0331..b3011dbfa7 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/3.0.7/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.8/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/sh2peaks.rst b/docs/reference/commands/sh2peaks.rst index 2795797a34..496061036a 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/3.0.7/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.8/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/sh2power.rst b/docs/reference/commands/sh2power.rst index 3380034496..fdf83a0e52 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/3.0.7/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.8/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/sh2response.rst b/docs/reference/commands/sh2response.rst index d4a9d559f2..b928a40a66 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/3.0.7/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.8/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/shbasis.rst b/docs/reference/commands/shbasis.rst index a9ec65d2c2..d34951f519 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/3.0.7/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.8/concepts/spherical_harmonics.html Options ------- diff --git a/docs/reference/commands/shconv.rst b/docs/reference/commands/shconv.rst index e67e876b72..40139d5042 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/3.0.7/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.8/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/3.0.7/concepts/spherical_harmonics.html +https://mrtrix.readthedocs.io/en/3.0.8/concepts/spherical_harmonics.html Options -------