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Co-authored-by: Samuel Guay <samuel.guay@umontreal.ca>

docs/how-to/use-advanced-commands.md

@@ -1,4 +1,4 @@
-# Advanced configuration and command
+# Advanced configuration and commands
 
 ## How to use advanced configuration
 
@@ -45,7 +45,7 @@ same level as the `"description"` entry.
 }
 ```
 
-### custom_entities combined with extractors
+### `custom_entities` combined with extractors
 
 default: None
 
@@ -59,15 +59,15 @@ entities directly into the final filename. custom_entities can be a list that
 combined extractor keys and regular entities. If key is `task` it will
 automatically add the field "TaskName" inside the sidecase file.
 
-### search_method
+### `search_method`
 
 default: `"search_method": "fnmatch"`
 
 fnmatch is the behaviour (See criteria) by default and the fall back if this
 option is set incorrectly. `re` is the other choice if you want more flexibility
 to match criteria.
 
-### dup_method
+### `dup_method`
 
 default: `"dup_method": "run"`
 
@@ -79,14 +79,14 @@ customEntities of the other acquisitions. This behavior is a
 [heudiconv](https://heudiconv.readthedocs.io/en/latest/changes.html) inspired
 feature.
 
-### case_sensitive
+### `case_sensitive`
 
 default: `"case_sensitive": "true"`
 
 If false, comparisons between strings/lists will be not case sensitive. It's
 only disabled when used with `"search_method": "fnmatch"`.
 
-### post_op
+### `post_op`
 
 default: `"post_op": []`
 
@@ -132,21 +132,21 @@ which datatype is fmap.
 Finally, this is a template string and dcm2bids will replace `src_file` and
 `dst_file` by the source file (input) and the destination file (output).
 
-### dcm2niixOptions
+### `dcm2niixOptions`
 
 default: `"dcm2niixOptions": "-b y -ba y -z y -f '%3s_%f_%p_%t'"`
 
 Arguments for dcm2niix
 
-### compKeys
+### `compKeys`
 
 default: `"compKeys": ["SeriesNumber", "AcquisitionTime", "SidecarFilename"]`
 
 Acquisitions are sorted using the sidecar data. The default behaviour is to sort
 by `SeriesNumber` then by `AcquisitionTime` then by the `SidecarFilename`. You
 can change this behaviour setting this key inside the configuration file.
 
-### criteria
+### `criteria`
 
 #### Handle multi site filtering
 
@@ -247,7 +247,7 @@ command.
 
     ```
 
-### --auto_extract_entities
+### `--auto_extract_entities`
 
 This option will automatically try to find 3 entities (task, dir and echo) for
 specific datatype/suffix.
@@ -312,7 +312,7 @@ like this.
 :radioactive: You can find more detailed information by looking at the file [`dcm2bids/utils/utils.py`](../dcm2bids/utils/utils/) and
 more specifically *`auto_extractors`* and *`auto_entities`* variables.
 
-### --bids_validate
+### `--bids_validate`
 
 By default, dcm2bids will not validate your final BIDS structure. If needed, you
 can install