From 0f9d8a78188bb8a33a2e06c55e5d636e7ba8aa69 Mon Sep 17 00:00:00 2001 From: Kay Robbins <1189050+VisLab@users.noreply.github.com> Date: Sat, 20 Jan 2024 07:46:09 -0600 Subject: [PATCH] Minor typo and link corrections in the docs --- docs/source/FileRemodelingTools.md | 4 ++-- docs/source/HedConditionsAndDesignMatrices.md | 10 +++++----- docs/source/HedGovernance.md | 2 +- docs/source/HedMatlabTools.md | 8 ++++---- docs/source/HedPythonTools.md | 6 +++--- docs/source/HedSearchGuide.md | 7 ++++--- docs/source/HedTestDatasets.md | 2 +- docs/source/HowCanYouUseHed.md | 8 ++++---- docs/source/IntroductionToHed.md | 2 +- 9 files changed, 25 insertions(+), 24 deletions(-) diff --git a/docs/source/FileRemodelingTools.md b/docs/source/FileRemodelingTools.md index 24f63bf..5f62fbd 100644 --- a/docs/source/FileRemodelingTools.md +++ b/docs/source/FileRemodelingTools.md @@ -333,9 +333,9 @@ Users are free to use either form. > The name(s) of the tasks to be included (for BIDS-formatted files only). > When a dataset includes multiple tasks, the event files are often structured > differently for each task and thus require different transformation files. -> This option allows the backups and operations to be restricted to a individual tasks. +> This option allows the backups and operations to be restricted to an individual task. -> If this option is omitted, all tasks are used. This means that all `events.tsv` files are +> If you omit this option, all tasks are used. This means that all `events.tsv` files are > restored from a backup if the backup is used, the operations are performed on all `events.tsv` files, and summaries are combined over all tasks. > If a list of specific task names follows this option, only datafiles corresponding to diff --git a/docs/source/HedConditionsAndDesignMatrices.md b/docs/source/HedConditionsAndDesignMatrices.md index d6223be..06d7582 100644 --- a/docs/source/HedConditionsAndDesignMatrices.md +++ b/docs/source/HedConditionsAndDesignMatrices.md @@ -21,7 +21,7 @@ of factor vectors and experimental design if you are unfamiliar with these topic * [**HED annotations for conditions**](hed-annotations-for-conditions-anchor) * [**Direct condition variables**](direct-condition-variables-anchor) * [**Defined condition variables**](defined-condition-variables-anchor) - * [**Direct vs defined approaches**](direct-vs-defined-approaches-anchor)) + * [**Direct vs defined approaches**](direct-vs-defined-approaches-anchor) * [**Column vs row annotations**](column-vs-row-annotations-anchor) * [**Experimental design concepts**](experimental-design-concepts-anchor) * [**Design matrices and factor variables**](design-matrices-and-factor-variables-anchor) @@ -93,7 +93,7 @@ corresponding HED annotation into a single string representing the annotation fo Annotations without #'s are used directly, while annotations with # have the corresponding column values substituted when the annotation is assembled. -Example 3 shows the Hed annotation for the first row in the `events.tsv` file of Example 1. +Example 3 shows the HED annotation for the first row in the `events.tsv` file of Example 1. ````{admonition} Example 3: HED annotation for first event in Example 1 using JSON sidecar of Example 2. :class: tip @@ -106,7 +106,7 @@ Example 3 shows the Hed annotation for the first row in the `events.tsv` file of Notice that *Building/House* is a partial path rather than a single tag. This is because *House* is currently not part of the base HED vocabulary. However, users are allowed to extend tags at most nodes in the HED schema, -but they must use a path that includes a least one ancestor in the HED schema. +but they must use a path that includes at least one ancestor in the HED schema. HED tools have the capability of automatically detecting *Condition-variable* tags in annotated HED datasets to create factor vectors and summaries automatically. @@ -526,8 +526,8 @@ so any of the three possible encodings: categorical, ordinal, or one-hot can be Traditional neuroimaging experiments are carefully designed to control and document the external conditions under which the experiment is conducted. -Often a few items such as the task or the properties of a stimulus are -systematically varied as the stimulus is presented and participant responses +Often an experiment varies a few items such as the task or the properties of a stimulus +as the stimulus is presented and participant responses are recorded. For example, in an experiment to test for differences in diff --git a/docs/source/HedGovernance.md b/docs/source/HedGovernance.md index c3f50c8..7d1689a 100644 --- a/docs/source/HedGovernance.md +++ b/docs/source/HedGovernance.md @@ -212,7 +212,7 @@ organization site as indicated in the following table. | Python codebase | [hed-python](https://github.com/hed-standard/hed-python/issues) | Bug reports and feature requests. | | JavaScript codebase | [hed-javascript](https://github.com/hed-standard/hed-javascript/issues) | Bug reports and feature requests. | -HED also has a HED discussion group. (Subscribe by emailing: +HED also has a HED discussion group. Subscribe by emailing: [**hed-discussion+subscribe@googlegroups.com**](mailto:hed-discussion+subscribe@googlegroups.com). If you do not feel comfortable diff --git a/docs/source/HedMatlabTools.md b/docs/source/HedMatlabTools.md index 74b99ca..1bced03 100644 --- a/docs/source/HedMatlabTools.md +++ b/docs/source/HedMatlabTools.md @@ -50,8 +50,8 @@ Calling HED services from MATLAB requires the following steps: 1. Establish a session by requesting a CSRF token and a cookie. 2. Construct a header array using the token and the cookie. 2. **Create a request structure**. -5. **Make a request** using the MATLAB `webwrite`. -6. **Decode the response** returned from `webwrite`. +3. **Make a request** using the MATLAB `webwrite`. +4. **Decode the response** returned from `webwrite`. Usually, you will do the first step (the session setup) once at the beginning of your script to construct a fixed session header that can be used in subsequent requests in your script. @@ -267,7 +267,7 @@ If the sidecar had no errors, `results.data` will be an empty string. (eeglab-integration-anchor)= ## EEGLAB plug-in integration EEGLAB is the most widely used EEG software environment for analysis of -human electrophsyiological (and related) data. +human electrophysiological (and related) data. EEGLAB combines graphical and command-line user interfaces, making it friendly for both beginners who may who prefer a visual, and automated way of analyzing data as well as experts, @@ -316,7 +316,7 @@ Read a description of the dataset and of its included event codes by selecting: > **Edit --> About this dataset**: -I15about_this_dataset +I15about_this_dataset The description gives a general idea of the codes found in the event structure. Yet, inquisitive researchers interested in the nature of the stimuli diff --git a/docs/source/HedPythonTools.md b/docs/source/HedPythonTools.md index 26e8f8c..871cd31 100644 --- a/docs/source/HedPythonTools.md +++ b/docs/source/HedPythonTools.md @@ -144,7 +144,7 @@ You should only change the values in the **description** and the **HED** columns To use this notebook, you will need to provide the path to the JSON sidecar and a path to save the spreadsheet if you want to save it. If you don't wish to save the spreadsheet, assign `spreadsheet_filename` to be `None` -and the result is just printed.. +and the result is just printed. (summarize-events-anchor)= @@ -315,11 +315,11 @@ as the file key. For a file name `sub-001_ses-3_task-target_run-01_events.tsv`, the tuple ('sub', 'task') gives a key of `sub-001_task-target`, -while the tuple ('sub', 'ses', 'run) gives a key of `sub-001_ses-3_run-01`. +while the tuple ('sub', 'ses', 'run') gives a key of `sub-001_ses-3_run-01`. The use of dictionaries of file names with such keys makes it easier to associate related files in the BIDS naming structure. -Notice that specifying entities ('sub', 'ses', 'run) gives the +Notice that specifying entities ('sub', 'ses', 'run') gives the key `sub-001_ses-3_run-01` for all three files: `sub-001_ses-3_task-target_run-01_events.tsv`, `sub-001_ses-3_task-target_run-01_eeg.set` and `sub-001_ses-3_task-target_run-01_eeg.edf`. diff --git a/docs/source/HedSearchGuide.md b/docs/source/HedSearchGuide.md index 9bff91a..ff394cf 100644 --- a/docs/source/HedSearchGuide.md +++ b/docs/source/HedSearchGuide.md @@ -193,9 +193,10 @@ You can replace any term with a wildcard: | **`???`**
Matches any group | {`A` and `???`} | *(A, (B))* | *(A)
(B, C)
(A, B)* | -**Notes**: You cannot use negation inside exact matching groups "{X:}" or "{X:Y}" notation.
-You cannot use negation in combination with wildcards ( ?, ??, or ??? )
-In exact group matching, or matches one or the other, not both. eg. {A or B:} matches (A) or (B), but not (A, B) +**Notes**: You cannot use negation inside exact matching groups `{X:}` or `{X:Y}` notation.
+You cannot use negation in combination with wildcards ( `?`, `??`, or `???` )
+In exact group matching, `or` matches one or the other, not both: +`{A or B:}` matches `(A)` or `(B)`, but not `(A, B)` ## Where can HED search be used? diff --git a/docs/source/HedTestDatasets.md b/docs/source/HedTestDatasets.md index 11e78e9..8f9d618 100644 --- a/docs/source/HedTestDatasets.md +++ b/docs/source/HedTestDatasets.md @@ -6,7 +6,7 @@ a set of HED-annotated datasets in These datasets can be useful for: 1. Writing lightweight software tests. -1. Serving as examples of how to incorporate HED into BIDS-structured data. +2. Serving as examples of how to incorporate HED into BIDS-structured data. The datasets have **empty raw data files**. However, some data headers containing the metadata are still intact. diff --git a/docs/source/HowCanYouUseHed.md b/docs/source/HowCanYouUseHed.md index 302d4e3..3938b85 100644 --- a/docs/source/HowCanYouUseHed.md +++ b/docs/source/HowCanYouUseHed.md @@ -30,7 +30,7 @@ but rather on how data should be recorded and transformed to maximize its downst **Here are some topics of interest to experimenters:** * [**Planning and running an experiment**](planning-and-running-an-experiment-anchor) -* [**Post processing the data**](post-processing-the-data-anchor) +* [**Post-processing the data**](post-processing-the-data-anchor) The *Actionable event annotation and analysis in fMRI: A practical guide to event handling* preprint, which can be found at [**https://osf.io/93km8/**](https://osf.io/93km8/), @@ -135,7 +135,7 @@ to quickly get an overview of its contents. ### Post-processing the event data The information that first comes off the experimental logs is usually not directly usable for -sharing and analysis. A number of HED [**File remodeling tools**](./FileRemodelingTools.md) tools +sharing and analysis. A number of HED [**File remodeling tools**](./FileRemodelingTools.md) might be helpful for restructuring your first pass at the event files. The [**remap columns**](./FileRemodelingTools.md#remap-columns) transformation is @@ -336,8 +336,8 @@ and *Duration* together with the *Definition* tag. See [**Temporal scope**](http design, as well as other information such as task, and the experiment's temporal organization. See [**HED conditions and design matrices**](https://www.hed-resources.org/en/latest/HedConditionsAndDesignMatrices.html). -The [**Advanced annotation**](https://hed-specification.readthedocs.io/en/latest/05_Advanced_annotation.html)) chapter of the HED specification -explains the rules for using these more advanced concepts. +The [**Advanced annotation**](https://hed-specification.readthedocs.io/en/latest/05_Advanced_annotation.html) +chapter of the HED specification explains the rules for using these more advanced concepts. (checking-correctness-anchor)= ### Checking correctness diff --git a/docs/source/IntroductionToHed.md b/docs/source/IntroductionToHed.md index 4bf2cf7..b1f7d58 100644 --- a/docs/source/IntroductionToHed.md +++ b/docs/source/IntroductionToHed.md @@ -97,7 +97,7 @@ Current systems in neuroimaging experiments do not record events beyond simple n or text (Event type Target) labels whose more complete and precise meanings are known only to the experimenter(s). -A central goal of HED is to enable building of archives of brain imaging data in a +A central goal of HED is to enable building of archives of brain imaging data in an amenable to large scale analysis, both within and across studies. Such event-related analysis requires that the nature(s) of the recorded events be specified in a common language.