Merge pull request #350 from VisLab/develop

Minor typo and link corrections in the docs

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 

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 

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:
 [**[email protected]**](mailto:[email protected]).
 
 If you do not feel comfortable

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**:
 
-<img src="_static/images/I15about_this_dataset.png" alt="I15about_this_dataset" align="center" style="zoom:100%;" />
+<img src="_static/images/I15about_this_dataset.png" alt="I15about_this_dataset" style="zoom:100%;" />
 
 The description gives a general idea of the codes found in the event structure.
 Yet, inquisitive researchers interested in the nature of the stimuli

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`.

docs/source/HedSearchGuide.md

@@ -193,9 +193,10 @@ You can replace any term with a wildcard:
 | **`???`**<br/>Matches any group      | {`A` and `???`} | *(A, (B))*            | *(A)<br/>(B, C)<br/>(A, B)*   |
 
 
-**Notes**: You cannot use negation inside exact matching groups "{X:}" or "{X:Y}" notation. <br/>
-You cannot use negation in combination with wildcards ( ?, ??, or ??? )<br/>
-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. <br/>
+You cannot use negation in combination with wildcards ( `?`, `??`, or `???` )<br/>
+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?
 

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.

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

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.