[ENH] update validator page

docs/blog/posts/2023-07-06-steering-group-minutes.md

@@ -108,7 +108,7 @@ categories:
 -   Do we need to introduce a new term? We could stick with p-seg (probabilistic) and d-seg (deterministic)
 -   Should we add this Derivatives output to the website?
 -   Where should it go? Create a PR or multiple PRs?
--   Suggestion: integrate the BIDS derivatives guidelines piecemeal into the BID general derivatives spec
+-   Suggestion: integrate the BIDS derivatives guidelines piecemeal into the BID general derivatives specification
 -   Maybe not the BEPs table info - table could go to the BIDs extensions
 
 ### Imaging Neuroscience Response regarding BIDS 'badge'

docs/blog/posts/2024-01-11-steering-group-minutes.md

@@ -136,7 +136,7 @@ Github project is established with many ideas but there aren\'t many
 
 -   Revisiting how BIDS is defined beyond MRI may be a path to improving
     adoption within the neuroscience community. Meaning BIDS started with
-    MRI and some of the BIDS spec might be more complicated than could
+    MRI and some of the BIDS specification might be more complicated than could
     have been if we had focused on all modalities from the start.
 
 -   iEEG, MEG, ...

docs/extensions/specific-guidelines.md

@@ -36,7 +36,7 @@ a repeated pattern in generating derivatives within several imaging modalities'
 
 1.  A reference map that is used to encode spatial features and parameters is required.
     There is an antecedent of this in `BIDS` with BEP23 ([see below](#BEP-23-PET-Derivatives)).
-    In that `BEP`, the proposed naming takes the pattern `_<suffix>ref` (for example `_boldref`, `_dwiref`...), and that solution has been suggested as a possibility in [issue #1532](https://github.com/bids-standard/bids-specification/issues/1532) of the spec repository.
+    In that `BEP`, the proposed naming takes the pattern `_<suffix>ref` (for example `_boldref`, `_dwiref`...), and that solution has been suggested as a possibility in [issue #1532](https://github.com/bids-standard/bids-specification/issues/1532) of the specification repository.
 
 1.  We have derived data that are no longer of the same type as the original,
     but for which we would like to keep the notion of the modality from which this was derived
@@ -57,7 +57,7 @@ and MUST specify the extension and metadata that are required with the suffix.
 
 1.  The file descriptor does fall under one of the generic derivatives descriptors.
 
-1.  No other descriptor exists in the `BIDS` spec.
+1.  No other descriptor exists in the `BIDS` specification.
     For example, `statmap` cannot be used, because it is already being used, or soon to be,
     for a [different specification](https://bids-standard.github.io/stats-models/walkthrough-1.html#from-run-outputs-to-subject-inputs).
 

docs/getting_started/folders_and_files/metadata.md

@@ -557,7 +557,7 @@ df.to_csv('my_new_file.tsv', sep='\t')
 
 -   Create a file with the following columns
     (at least, for other values see paragraph the
-    [BIDS spec](https://bids-specification.readthedocs.io/en/latest/03-modality-agnostic-files.html#participants-file))
+    [BIDS specification](https://bids-specification.readthedocs.io/en/latest/03-modality-agnostic-files.html#participants-file))
     -   participant_id
     -   age
     -   sex

docs/getting_started/tutorials/conversion/pet.md

@@ -997,7 +997,7 @@ and add the plasma series of data to it from our base text file:
 ![screenshot of unconverted sub-01_ses-testscan_recording-Manual_blood.tsv](https://i.imgur.com/VdFqh6H.png)
 
 Whoops, these numbers aren't in SI units, so we quickly convert time
-from minutes to seconds and Microcurie to Becquerel to conform to the spec.
+from minutes to seconds and Microcurie to Becquerel to conform to the specification.
 
 !!! note
 

docs/standards/schema/schema-rules.md

@@ -85,7 +85,7 @@
         run: optional
     ```
 
-    ![image of template rendered in spec](../../assets/img/noncontinuous_beh_rendered_template.png)
+    ![image of template rendered in specification](../../assets/img/noncontinuous_beh_rendered_template.png)
 
 ---
 

docs/tools/validator.md

@@ -5,18 +5,18 @@ that checks if a dataset is compliant with the BIDS standard.
 The validator is available for use within several different environments
 to best suit individual user preferences and use cases, those versions are:
 
--   A web browser based version
--   Command line version
--   Docker based version
--   A python library installable via pip
+-   [A web browser based version](https://bids-standard.github.io/bids-validator/)
+-   [Command line version](https://bids-validator.readthedocs.io/en/latest/user_guide/command-line.html)
+-   [Docker based version](https://hub.docker.com/r/bids/validator)
+-   A [python library](https://github.com/bids-standard/python-validator) installable from [pypi](https://pypi.org/project/bids-validator/) or [conda-forge](https://anaconda.org/conda-forge/bids-validator)
 
 Instructions to install and use these versions can be found
 within the [quickstart guide](https://github.com/bids-standard/bids-validator)
 at the BIDS Validator repository.
 
 ## Data Privacy and Confidentiality
 
-Please note that the web app is entirely browser(not server) based.
+Please note that the web app is entirely browser (not server) based.
 As such, there is no file uploading as part of the validation.
 
 ## Browser Version
@@ -25,7 +25,7 @@ As such, there is no file uploading as part of the validation.
     It requires that you use the Chrome or Firefox browser,
     since those are the only ones in which you can select a whole folder rather than individual files.
 
-    ![home](../assets/img/YD38eTE.png)
+    ![home](https://github.com/bids-standard/bids-validator/raw/main/docs/_static/web_entrypoint_dark.png#gh-dark-mode-only)
 
 1.  You can then choose the **folder** that you wish to validate
 
@@ -36,126 +36,91 @@ As such, there is no file uploading as part of the validation.
     This response indicates that your dataset is not BIDS compliant.
     Try following the suggestions listed to make the appropriate corrections.
 
-    ![Error](../assets/img//PEz9hbd.png)
+    ![Error](../assets/img/validator_error.png)
 
 !!! warning
 
     This response indicates that your dataset is BIDS compliant,
     but there are some non-critical problems
-    (such as optional fields missing, or differences between participants).
+    (such as recommended fields missing, or differences between participants).
 
-    ![Warning](../assets/img//Gqwc1q9.png)
+    ![Warning](../assets/img/validator_warning.png)
 
 !!! success "Success :rocket:"
 
     This response indicates that your folder contains a valid BIDS Dataset!
 
-    ![Valid](../assets/img/DPFVXOR.png)
+    <!-- ![Valid](../assets/img/DPFVXOR.png) -->
 
 ## Command Line Version
 
 ### Verifying a BIDS compliant data set
 
-After [installation with npm](https://github.com/bids-standard/bids-validator)
+After [installation with deno](https://bids-validator.readthedocs.io/en/latest/user_guide/command-line.html#using-the-command-line)
 using the CLI is relatively simple.
 Locate a bids data set similar to the one below:
 
 ```bash
-user@host:~/bids-examples$ tree sub001/
+user@host:~/bids-examples$ tree pet001
 
 sub001/
 ├── dataset_description.json
 ├── participants.json
 ├── participants.tsv
 ├── README
 └── sub-01
-    ├── ses-baseline
-    │   ├── anat
-    │   │   ├── sub-01_ses-baseline_T1w.json
-    │   │   └── sub-01_ses-baseline_T1w.nii.gz
-    │   └── pet
-    │       ├── sub-01_ses-baseline_pet.json
-    │       └── sub-01_ses-baseline_pet.nii.gz
-    └── ses-intervention
+    └── ses-01
         ├── anat
-        │   ├── sub-01_ses-intervention_T1w.json
-        │   └── sub-01_ses-intervention_T1w.nii.gz
+        │   ├── sub-01_ses-01_T1w.json
+        │   └── sub-01_ses-01_T1w.nii
         └── pet
-            ├── sub-01_ses-intervention_task-eyes_events.json
-            ├── sub-01_ses-intervention_task-eyes_events.tsv
-            ├── sub-01_ses-intervention_task-eyes_pet.json
-            └── sub-01_ses-intervention_task-eyes_pet.nii.gz
+            ├── sub-01_ses-01_trc-CIMBI36_pet.json
+            ├── sub-01_ses-01_trc-CIMBI36_pet.nii.gz
+            ├── sub-01_ses-01_trc-CIMBI36_recording-autosampler_blood.json
+            ├── sub-01_ses-01_trc-CIMBI36_recording-autosampler_blood.tsv
+            ├── sub-01_ses-01_trc-CIMBI36_recording-manual_blood.json
+            └── sub-01_ses-01_trc-CIMBI36_recording-manual_blood.tsv
 ```
 
-Now simply point the bids validator at the folder path of the subject(s) in
-question:
+Now simply point the bids validator at the folder path of the subject(s) in question:
 
 ```bash
-user@host:~/bids-examples$ bids-validator sub001
+user@host:~/bids-examples$ bids-validator pet001
 ```
 
 ### Types of Feedback
 
 !!! failure "Error"
 
-    As is the case w/ the browser or any version of the validator follow
-    the `[ERR]` messages and correct until bids-validator returns 0 errors after running.
+    As is the case with the browser or any version of the validator follow
+    the `[ERROR]` messages and correct until bids-validator returns 0 errors after running.
 
     ```bash
-    user@host:~/bids-examples$ bids-validator sub001
-
-    [email protected]
-
-    1: [ERR] Invalid JSON file. The file is not formatted according the schema. (code: 55 - JSON_SCHEMA_VALIDATION_ERROR)
-    ./sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.json
-    Evidence:  should have property InjectedRadioactivityUnits when property InjectedRadioactivity is present
-    ./sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.json
-    Evidence:  should have required property 'InjectedMassUnits'
-    ...
-                    ...
-    ... and 3 more files having this issue (Use --verbose to see them all).
-
-    Please visit https://neurostars.org/search?q=JSON_SCHEMA_VALIDATION_ERROR for existing conversations about this issue.
-
-
-            Summary:                Available Tasks:        Available Modalities:
-            14 Files, 5.72MB                                T1w
-            1 - Subject                                     pet
-            2 - Sessions                                    events
-
+    [ERROR] NIFTI_HEADER_UNREADABLE We were unable to parse header data from this NIfTI file. Please ensure it is not corrupted or mislabeled.
+                /sub-01/ses-01/anat/sub-01_ses-01_T1w.nii
 
-    If you have any questions, please post on https://neurostars.org/tags/bids.
+        Please visit https://neurostars.org/search?q=NIFTI_HEADER_UNREADABLE for existing conversations about this issue.
     ```
 
 !!! warning
 
     As stated with the browser version above, one may elect to ignore warnings,
     but the information provided via the validator should help to pinpoint
     where and how to resolve some of these warnings.
-    When in doubt consult the [BIDS Spec](https://bids-specification.readthedocs.io/en/latest/)
+    When in doubt consult the [BIDS specification](https://bids-specification.readthedocs.io/en/latest/)
 
     ```bash
-    user@host:~/bids-examples$ bids-validator sub001/
+    [WARNING] JSON_KEY_RECOMMENDED A JSON file is missing a key listed as recommended.
+                DatasetType
+                /dataset_description.json
 
-    [email protected]
+                GeneratedBy
+                /dataset_description.json
 
-    1: [WARN] Tabular file contains custom columns not described in a data dictionary (code: 82 - CUSTOM_COLUMN_WITHOUT_DESCRIPTION)
-    ./sub-01/func/sub-01_task-balloonanalogrisktask_run-01_events.tsv
-                    ...
-                    ...
-    ... and 38 more files having this issue (Use --verbose to see them all).
+                SourceDatasets
+                /dataset_description.json
 
-    Please visit https://neurostars.org/search?q=CUSTOM_COLUMN_WITHOUT_DESCRIPTION for existing conversations about this issue.
-
-
-            Summary:                   Available Tasks:                Available Modalities:
-            134 Files, 411.53KB        balloon analog risk task        T1w
-            16 - Subjects                                              inplaneT2
-            1 - Session                                                bold
-                                                                    events
-
-
-    If you have any questions, please post on https://neurostars.org/tags/bids.
+        Please visit https://neurostars.org/search?q=JSON_KEY_RECOMMENDED for existing conversations about this issue.
     ```
 
 !!! success "Success :rocket:"
@@ -164,15 +129,10 @@ user@host:~/bids-examples$ bids-validator sub001
 
     ```bash
     user@host:~/bids-examples$ bids-validator sub001
-    [email protected]
-
-    This dataset appears to be BIDS compatible.
-
-            Summary:                  Available Tasks:        Available Modalities:
-            12 Files, 218.75KB                                T1w
-            1 - Subject                                       pet
-            1 - Session                                       blood
 
+          Summary:                         Available Tasks:        Available Modalities:
+          12 Files, 224 kB                                         PET
+          1 - Subjects 1 - Sessions                                MRI
 
-    If you have any questions, please post on https://neurostars.org/tags/bids
+        If you have any questions, please post on https://neurostars.org/tags/bids.
     ```

mkdocs.yml

@@ -137,10 +137,10 @@ nav:
         -   getting_started/templates/index.md
 -   Tools:
     -   tools/index.md
+    -   tools/converters.md
     -   tools/validator.md
     -   tools/bids-apps.md
     -   tools/others.md
-    -   tools/converters.md
 -   Datasets:
     -   datasets/index.md
 -   FAQ: