correct markdown formatting

README.md

@@ -7,45 +7,47 @@ The above publication also introduces the software
 > Collaborative Brain Wave Analysis Pipeline (Cobrawap). RRID:SCR_022966. [https://cobrawap.readthedocs.io](https://cobrawap.readthedocs.io)
 
 ## How to reproduce the results/figures from the publication
-#### Setup
+
+### Setup
 - Setup the Python environment (`conda create -f environment.yaml`) and activate it.
 - Setup Cobrawap with `cobrawap init` and follow the instructions to 
     - set the cobrawap output path (\<cobrawap_output\>),
     - set the cobrawap config path (\<cobrawap_configs\>)
     (see also the [documentation](https://cobrawap.readthedocs.io)).
-- Set the local project paths in *project_utils/project_paths.py*.
+- Set the local project paths in *project\_utils/project\_paths.py*.
+
 
-#### Get the data
+### Get the data
 - Download the ECoG (IDIBAPS) and calcium imaging (LENS) datasets from the EBRAINS KnowledgeGraph:
-    - IDIBAPS_WBS: [doi:10.25493%2FDZWT-1T8](https://doi.org/10.25493%2FDZWT-1T8)
-    - IDIBAPS_FXS: [doi:10.25493/ANF9-EG3](https://doi.org/10.25493/ANF9-EG3)
-    - IDIBAPS_PM: [10.25493/WKA8-Q4T](https://doi.org/10.25493/WKA8-Q4T)
-    - LENS_M: [10.25493/QFZK-FXS](https://doi.org/10.25493/QFZK-FXS)
-    - LENS_ISO: [10.25493/XJR8-QCA](https://doi.org/10.25493/XJR8-QCA)
-- Set the path parameter (`DATA_SETS`) in the *stage01_data_entry/config/config_<profile>.yaml* files to the corresponding data locations.
-
-#### Run the analysis pipeline
-- To produce all the possible pipeline outputs *\<cobrawap_output\>/\<profile\>\<variant\>/stage05_(channel_)wave_characterization/\<event-type\>_\<measure-type\>_measures.csv*, set the event-type and measure-type accordingly and execute:
+    - IDIBAPS\_WBS: [doi:10.25493%2FDZWT-1T8](https://doi.org/10.25493%2FDZWT-1T8)
+    - IDIBAPS\_FXS: [doi:10.25493/ANF9-EG3](https://doi.org/10.25493/ANF9-EG3)
+    - IDIBAPS\_PM: [10.25493/WKA8-Q4T](https://doi.org/10.25493/WKA8-Q4T)
+    - LENS\_M: [10.25493/QFZK-FXS](https://doi.org/10.25493/QFZK-FXS)
+    - LENS\_ISO: [10.25493/XJR8-QCA](https://doi.org/10.25493/XJR8-QCA)
+- Set the path parameter (`DATA\_SETS`) in the *stage01\_data\_entry/config/config\_<profile>.yaml* files to the corresponding data locations.
+
+### Run the analysis pipeline
+- To produce all the possible pipeline outputs *\<cobrawap\_output\>/\<profile\>\<variant\>/stage05\_(channel\_)wave\_characterization/\<event-type\>\_\<measure-type\>\_measures.csv*, set the event-type and measure-type accordingly and execute:
 ```
 cobrawap run --profile=<profile>
 ```
 
-**Profiles:** The names that are used for the individual recordings and their corresponding configurations are listed in *project_utils/profiles.txt*.
+**Profiles:** The names that are used for the individual recordings and their corresponding configurations are listed in *project\_utils/profiles.txt*.
 
 **Variants:** Variants are alternative configurations for a profile and can be specified by appending a corresponding label to the profile with a '|', e.g. `<profile>|minimatrigger`. Here, additional variants for spatial downsampling and alternative trigger detection are applied to all LENS datasets: **|macrodim3**, **|macrodim5**, **|macrodim7**, **|macrodim9**, **|macrodim11**, **|minimatrigger**.
 
-**Measure types:** There are two alternative final stages of the pipeline *stage05_wave_characterization* and *stage05_channel_wave_characterization*, corresponding to calculating either **wave-wise** or **channel-wise** characteristic measures. You can select between them in the top-level pipeline config *\<cobrawap_configs\>/configs/config.yaml*.
+**Measure types:** There are two alternative final stages of the pipeline *stage05\_wave\_characterization* and *stage05\_channel\_wave\_characterization*, corresponding to calculating either **wave-wise** or **channel-wise** characteristic measures. You can select between them in the top-level pipeline config *\<cobrawap\_configs\>/configs/config.yaml*.
 
 **Event types:** The wave characterization in the pipeline output can be either given for all **wavefronts** or all **wavemodes** (wavemode = average of similar wavefronts). You can select between them by setting the parameter `EVENT_NAME` in the corresponding *stage05* config file. Also change the prefix of the `STAGE_OUTPUT` accordingly as `wavefronts` or `wavemodes`.
 
-#### Aggregate the output of the analysis pipeline
-In the folder *aggregate_pipeline_output* run snakemake (`snakemake -c1`) to create the combined dataframes from the individual pipeline outputs:
-    - *\<event-type\>_\<measure-type\>\<variant\>_measures.csv* containing the pipeline outputs for all profiles,
-    - *wavefronts_\<measure-type\>_trend_measures.csv* containing the moments of each measure for the downsampled (|macrodim) calcium imaging data,
-    - *wavemodes_\<measure-type\>_avg_measures.csv* containing the measures per wavefront averaged for each wavemode.
+### Aggregate the output of the analysis pipeline
+In the folder *aggregate\_pipeline\_output* run snakemake (`snakemake -c1`) to create the combined dataframes from the individual pipeline outputs:
+- *\<event-type\>\_\<measure-type\>\<variant\>\_measures.csv* containing the pipeline outputs for all profiles,
+- *wavefronts\_\<measure-type\>\_trend\_measures.csv* containing the moments of each measure for the downsampled (|macrodim) calcium imaging data,
+- *wavemodes\_\<measure-type\>\_avg\_measures.csv* containing the measures per wavefront averaged for each wavemode.
 
-#### Plot the figures
-In folder *plot_figures*:
+### Plot the figures
+In folder *plot\_figures*:
 - Run `snakemake -c1` to produce Figure 5 and 6.
 - Execute `plot_wavemodes_dashboard.ipynb` to produce Figure 4 and S3 (change profile name in notebook accordingly).
 - Execute `plot_trigger_detection_f-anesthesia.ipynb` to produce Figure S4.