diff --git a/.github/workflows/default.yml b/.github/workflows/default.yml index 45714f3..c2d62d3 100644 --- a/.github/workflows/default.yml +++ b/.github/workflows/default.yml @@ -2,7 +2,7 @@ name: Build Documentation on: push: - branches: + branches: - master jobs: @@ -36,4 +36,4 @@ jobs: branch: gh-pages directory: gh-pages github_token: ${{ secrets.GITHUB_TOKEN }} - # =============================== \ No newline at end of file + # =============================== diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index 413d276..e706e06 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -4,7 +4,7 @@ name: Build specification and publish # 2. Upload it to the Zenodo deposit (https://zenodo.org/record/5084789) ################################################################################# -# A number of variables must be set for the jobs to work. +# A number of variables must be set for the jobs to work. # # - ZENODO_URL: - Zenodo URL to deposit release file to. # diff --git a/.gitignore b/.gitignore index 00b8c91..b4b3f84 100644 --- a/.gitignore +++ b/.gitignore @@ -5,4 +5,3 @@ nifti_mrs_specification*.pdf explanatory_doc/_build .vscode/ ~$*.docx - diff --git a/README.md b/README.md index 6b80ae3..8b8bc45 100644 --- a/README.md +++ b/README.md @@ -87,4 +87,4 @@ We recommend using conda to download the packages, and using python >=3.7. ``` ## Licence -The content of this project itself is licensed under the [Creative Commons Attribution 4.0 International (CC BY 4.0) Licence](https://creativecommons.org/licenses/by/4.0/), any code within this repository is licensed under the BSD 3-Clause Licence. +The content of this project itself is licensed under the [Creative Commons Attribution 4.0 International (CC BY 4.0) Licence](https://creativecommons.org/licenses/by/4.0/), any code within this repository is licensed under the BSD 3-Clause Licence. diff --git a/data_conventions.ipynb b/data_conventions.ipynb index 649f7e0..996504a 100644 --- a/data_conventions.ipynb +++ b/data_conventions.ipynb @@ -362,7 +362,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Define a right-handed coordinate frame (right pannel): \n", + "Define a right-handed coordinate frame (right panel): \n", "![image.png](specification_images/right-handed_half.png)\n", "\n", "Define the x-axis to be the real component, y the imaginary component and z as time. \n", diff --git a/example_data/data_generation/example_01_manual_conversion_svs.ipynb b/example_data/data_generation/example_01_manual_conversion_svs.ipynb index 7480c63..fc45c3e 100755 --- a/example_data/data_generation/example_01_manual_conversion_svs.ipynb +++ b/example_data/data_generation/example_01_manual_conversion_svs.ipynb @@ -275,7 +275,7 @@ "The NIfTI-MRS standard includes definitions of some common MRS metadata. \n", "Though the use of it is optional, here we populate some of those fields for illustration. \n", " \n", - "Incude: \n", + "Include: \n", "**EchoTime**, double, Time from centroid of excitation to start of FID or centre of echo. Units: Seconds \n", "**RepetitionTime**, double, Sequence repetition time. Units: Seconds \n", "**InversionTime**, double, Inversion time. Units: Seconds \n", diff --git a/explanatory_doc/metadata.rst b/explanatory_doc/metadata.rst index a57f577..ae96a65 100644 --- a/explanatory_doc/metadata.rst +++ b/explanatory_doc/metadata.rst @@ -132,6 +132,3 @@ Example header extensions :align: center Extracts of NIfTI-MRS JSON-formatted header extensions for four different pieces of example data. The full example data is available from Zenodo_. Each example demonstrates a different aspect of the header extension format. Figure annotations are shown as blue italicised text. A: Structure of a header extension of 1H single-voxel data before pre-processing. B: Header extension for processed 31P MRSI, including fields that are marked for anonymisation (red). C: Example of dynamic header fields indicating an editing condition stored in the 7th dimension. D: Extract of the processing provenance in a MEGA-PRESS sequence pre-processed using FSL-MRS. - - - diff --git a/explanatory_doc/spatial_orient.rst b/explanatory_doc/spatial_orient.rst index 94a92ba..94a6f54 100644 --- a/explanatory_doc/spatial_orient.rst +++ b/explanatory_doc/spatial_orient.rst @@ -35,4 +35,4 @@ Occasionally multi-voxel (CSI, or MRSI) data will be acquired with additional si Image-selected in vivo spectroscopy (ISIS) ------------------------------------------ -The ISIS technique utilises alternating slice selective signal inversion schemes to achieve localisation in one, two or three dimensions. Each encoding can be stored as an element of a higher encoding dimensions with the tag ``DIM_ISIS``. Each encoding will have a different spatial localisation extent, but this is not encoded in NIfTI-MRS. Rather separate elements are stored for pre-processing purposes (e.g. frequency and phase alignment), but the localisation of each element is considered to tbe the same and the standard mechanism (as described above) is used. \ No newline at end of file +The ISIS technique utilises alternating slice selective signal inversion schemes to achieve localisation in one, two or three dimensions. Each encoding can be stored as an element of a higher encoding dimensions with the tag ``DIM_ISIS``. Each encoding will have a different spatial localisation extent, but this is not encoded in NIfTI-MRS. Rather separate elements are stored for pre-processing purposes (e.g. frequency and phase alignment), but the localisation of each element is considered to be the same and the standard mechanism (as described above) is used.