From 4cf0723ab04d255273b93957181291fa260b3a11 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Tue, 14 May 2024 13:50:28 -0700 Subject: [PATCH 1/3] Apply US spelling. Addresses current codespell CI failure. --- src/derivatives/05-diffusion-derivatives.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/derivatives/05-diffusion-derivatives.md b/src/derivatives/05-diffusion-derivatives.md index fc8d6633..8b6867f8 100644 --- a/src/derivatives/05-diffusion-derivatives.md +++ b/src/derivatives/05-diffusion-derivatives.md @@ -40,7 +40,7 @@ that warrant explicit mention due to their consequence in how they are represent - The encoding of *anisotropic* information; that is, quantities for which the value depends on the orientation in which it is sampled. Much of the detail in diffusion derivatives is therefore dedicated - to the definition of how such data are serialised into corresponding NIfTI images, + to the definition of how such data are serialized into corresponding NIfTI images, and how corresponding metadata is used to facilitate correct interpretation of those data. - A diffusion model may represent the contents of each image voxel as the sum of *multiple compartments*; @@ -268,7 +268,7 @@ Dictionary `"Model["Parameters"]"` has the following reserved keywords that may | **Key name** | **Description** | | ---------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| FitMethod | OPTIONAL. String. The optimization procedure used to fit the intrinsic model parameters to the empirical diffusion-weighted signal. Resrved values are: "`ols`" (Ordinary Least Squares); "`wls`" (Weighted Least Squares); "`iwls`" (Iterative Weighted Least Squares); "`nlls`" (Non-Linear Least Squares). | +| FitMethod | OPTIONAL. String. The optimization procedure used to fit the intrinsic model parameters to the empirical diffusion-weighted signal. Reserved values are: "`ols`" (Ordinary Least Squares); "`wls`" (Weighted Least Squares); "`iwls`" (Iterative Weighted Least Squares); "`nlls`" (Non-Linear Least Squares). | | Iterations | OPTIONAL. Integer. The number of iterations used for any form of model fitting procedure where the number of iterations is a fixed input parameter. | | OutlierRejectionMethod | OPTIONAL. String. Text describing any form of rejection of outlier values that was performed during fitting of the model. | | Samples | OPTIONAL. Integer. The number of realisations of a diffusion model from which statistical summaries (e.g. mean, standard deviation) of those parameters were computed. | @@ -282,9 +282,9 @@ Some fields are applicable only to specific [orientation encoding types](#orient | ------------------- | ------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | BootstrapAxis | Any | OPTIONAL. Integer. If multiple realisations of a given parameter are stored in a NIfTI image, this field nominates the image axis (indexed from zero) along which those multiple realisations are stored. | | Description | Any | OPTIONAL. String. Text description of what model parameter is encoded in the corresponding data file. | -| NonNegativity | All except [spherical coordinates](#encoding-spherical) and [3-vectors](#encoding-3vector) | OPTIONAL. String. Options are: { `regularized`, `constrained` }. Specifies whether, during model fitting, the parameter was regularised to not take extreme negative values, or was explicitly forbidden from taking negative values. | +| NonNegativity | All except [spherical coordinates](#encoding-spherical) and [3-vectors](#encoding-3vector) | OPTIONAL. String. Options are: { `regularized`, `constrained` }. Specifies whether, during model fitting, the parameter was regularized to not take extreme negative values, or was explicitly forbidden from taking negative values. | | OrientationEncoding | Any | REQUIRED if dimensionality of NIfTI image is greater than three. Dictionary. Provides information requisite to the interpretation of orientation information encoded in each voxel; more details below. | -| ResponseFunction | [Spherical harmonics](#encoding-sh) | OPTIONAL. Dictionary. Specifies a response function that was utilised by a deconvolution algorithm; more details below. | +| ResponseFunction | [Spherical harmonics](#encoding-sh) | OPTIONAL. Dictionary. Specifies a response function that was utilized by a deconvolution algorithm; more details below. | Dictionary `"OrientationEncoding"` has the following reserved keywords: @@ -321,7 +321,7 @@ Dictionary `"ResponseFunction"` has the following reserved keywords: - List of lists of floating-point values. One list per unique *b*-value. Each individual list contains a coefficient per even zonal spherical harmonic degree starting from zero. - If the response function utilised has a different number of non-zero zonal spherical harmonic coefficients for different *b*-values, + If the response function utilized has a different number of non-zero zonal spherical harmonic coefficients for different *b*-values, these must be padded with zeroes such that all lists contain the same number of floating-point values. ### Demonstrative examples @@ -780,10 +780,10 @@ Dictionary `"ResponseFunction"` has the following reserved keywords: Notes: - - Here the descriptors "`merged`" and "`mean`" have been utilised + - Here the descriptors "`merged`" and "`mean`" have been utilized to distinguish between the comprehensive set of all bootstrap realisations and the computed mean statistics of parameters across all realisations respectively, - as this is the terminology utilised by the FSL software itself. + as this is the terminology utilized by the FSL software itself. These labels are not however a part of the specification. - Care must be taken for images of greater than three dimensions From 1317863ad7aec9beb504c47becc95cc6b4df3791 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Tue, 14 May 2024 13:53:15 -0700 Subject: [PATCH 2/3] Markdown table linting --- src/derivatives/05-diffusion-derivatives.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/derivatives/05-diffusion-derivatives.md b/src/derivatives/05-diffusion-derivatives.md index 8b6867f8..761e19c7 100644 --- a/src/derivatives/05-diffusion-derivatives.md +++ b/src/derivatives/05-diffusion-derivatives.md @@ -891,9 +891,9 @@ Dictionary `"ResponseFunction"` has the following reserved keywords: *N* = ((*lmax*+1) x (*lmax*+2)) / 2 - | ***lmax*** | 0 | 2 | 4 | 6 | 8 | 10 | ... | + | ***lmax*** | 0 | 2 | 4 | 6 | 8 | 10 | ... | | --------------------- |--:|--:|--: |--: |--: |--: | :--: | - | ***N*** | 1 | 6 | 15 | 28 | 45 | 66 | ... | + | ***N*** | 1 | 6 | 15 | 28 | 45 | 66 | ... | - Relationship between maximal degree of *zonal* spherical harmonic function (spherical harmonics function where all *m* != 0 terms are @@ -902,6 +902,6 @@ Dictionary `"ResponseFunction"` has the following reserved keywords: *N* = 1 + (*lmax* / 2) - | ***lmax*** | 0 | 2 | 4 | 6 | 8 | 10 | ... | + | ***lmax*** | 0 | 2 | 4 | 6 | 8 | 10 | ... | | --------------------- |--:|--:|--:|--:|--:|--: | :--: | - | ***N*** | 1 | 2 | 3 | 4 | 5 | 6 | ... | + | ***N*** | 1 | 2 | 3 | 4 | 5 | 6 | ... | From 77dbfbd718b8c3c380d8e630c92aea401eb37115 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Tue, 14 May 2024 13:54:28 -0700 Subject: [PATCH 3/3] Get rid of a few latin phrases (i.e., "e.g."). --- src/derivatives/05-diffusion-derivatives.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/derivatives/05-diffusion-derivatives.md b/src/derivatives/05-diffusion-derivatives.md index 761e19c7..703ef717 100644 --- a/src/derivatives/05-diffusion-derivatives.md +++ b/src/derivatives/05-diffusion-derivatives.md @@ -82,7 +82,7 @@ that warrant explicit mention due to their consequence in how they are represent how data across dimensions beyond the three spatial dimensions are to be interpreted. In cases where a pipeline yields only a single parameter from a model, -entity "`_param-