From d00e2ddb11aba101f179ce87cbefe178a73f29b3 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Sun, 17 Jul 2022 11:30:21 +0200 Subject: [PATCH 1/2] Fix typos found by codespell --- data_conventions.ipynb | 2 +- .../data_generation/example_01_manual_conversion_svs.ipynb | 2 +- explanatory_doc/spatial_orient.rst | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) 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/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. From 45650a0277b16f791622bb51e8c81658994b47ac Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Sun, 17 Jul 2022 11:35:10 +0200 Subject: [PATCH 2/2] Remove spurious trailing spaces and empty lines --- .github/workflows/default.yml | 4 ++-- .github/workflows/release.yaml | 2 +- .gitignore | 1 - README.md | 2 +- explanatory_doc/metadata.rst | 3 --- 5 files changed, 4 insertions(+), 8 deletions(-) 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/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. - - -