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docs/protocols/protocols_guide_internal-how-1.md

@@ -31,7 +31,7 @@ nav_order: 3
 ## 1. Prepare the required files
 
 ### 1.1 Ask your radiographer for your protocol pdf and scanning procedure file.
-Your scanning procedure file (.doc) and scanner protocol (.pdf) will be given to by your radiographer at the start of your project. You will be provided with a new version if there are changes in the protocol. You can request copies of these files by emailing radiographers@win.ox.ac.uk with your calpendo project number.
+Your scanning procedure file (.doc) and scanner protocol (.pdf) will be given to you by your radiographer at the start of your project. You will be provided with a new version if there are changes in the protocol. You can request copies of these files by emailing radiographers@win.ox.ac.uk with your calpendo project number.
 
 ### 1.2 Request permission from the radiographer author of the scanning procedure to add them as an author on the public doi record of your protocol.
 The radiographer author of your scanning procedure is listed at the top of the file. Contact this radiographer and ask their permission to be listed as a contributor to this protocol on the public doi record. Request the radiographers ORCID ID for inclusion.
@@ -55,8 +55,8 @@ Only WIN members (as determined by SSO authentication) are able to deposit proto
 
 To log in:
 1. Go to [https://open.win.ox.ac.uk/protocols/](https://open.win.ox.ac.uk/protocols/)
-2. Click the "Login" icon on the top right of the screen
-3. Click the "Login via Shibboleth" option and enter your Oxford SSO details when requested.
+2. Click the `Login` icon on the top right of the screen
+3. Click the `Login via Shibboleth` option and enter your Oxford SSO details when requested.
 
 
 
@@ -66,16 +66,16 @@ Protocols are saved to individual user profiles.
 
 ![gif - add new protocol](../../../img/img-protocols/gif_add-protocol.gif)
 
-1.  Once you are logged in, you will see the "**Add Protocol**" icon.
-2. Click on "**Add Protocol**", and you will be taken to the "**Add new protocol**"" page.
-3.  Click the "**Browse**" button to open a file explorer.
-4.  Navigate in the file explorer to the scanner protocol (.pdf) you want to upload. Select "open" in your file explorer.
-5. Click on the "**Add new protocol**" button to upload the selected pdf to the database.
+1. Once you are logged in, you will see the `Add Protocol` icon.
+2. Click on `Add Protocol`, and you will be taken to the `Add new protocol` page.
+3. Click the `Browse` button to open a file explorer.
+4. Navigate in the file explorer to the scanner protocol (.pdf) you want to upload. Select `open` in your file explorer.
+5. Click on the `Add new protocol` button to upload the selected pdf to the database.
 
 
 
 ### 2.3 File type error
-If the uploaded file is recognised as a sequence pdf, you should see the **Register Protocol** page. If the file is not in the right format, you will see an error. Please check the file you have selected is a pdf of your MR protocol.
+If the uploaded file is recognised as a sequence pdf, you should see the `Register Protocol` page. If the file is not in the right format, you will see an error. Please check the file you have selected is a pdf of your MR protocol.
 
 ## 3. Top level protocol information
 You can enter details about your protocol which are relevant to the study as a whole, or all sequences. These details are entered at the top of your protocol. These details will help future users understand your decisions or implement your protocol.
@@ -121,7 +121,7 @@ Browse to and add any attachments to support the implementation of your protocol
 *Note that there is a file size limit of 15MB for each individual file attached*
 
 ## 5. Sequence level protocol information
-You can add details specific to individual sequences. These details may make it easier for users of this protocol to understand the outputs if the protocol is run, information about why these sequences where chosen or refer to decisions made during pilotting. You may reference back to earlier versions of the protocol entry to indicate changes where appropriate.
+You can add details specific to individual sequences. These details may make it easier for users of this protocol to understand the outputs if the protocol is run. You can include information about why these sequences where chosen or refer to decisions made during pilotting. You may reference back to earlier versions of the protocol entry to indicate changes where appropriate.
 
 Each of the sections below should be completed for each sequence.
 
@@ -131,10 +131,10 @@ Each of the sections below should be completed for each sequence.
 This is identified from the pdf. You can update it or add any additional context where necessary.
 
 ### 5.1 Sequence keywords
-1. Keywords including for example modality, ROIs, clinical conditions, study population, study type.
+Keywords including for example modality, ROIs, clinical conditions, study population, study type.
 
 ### 5.2 Sequence description
-The sequence description provides key features that might help someone choose whether it meets their needs. For example, “A standard T1-weighted structural scan, of 1mm isotropic resolution, suitable for registration to a standard template in an FMRI protocol.".
+The sequence description provides key features that might help someone choose whether it meets their needs. For example, “A standard T1-weighted structural scan, of 1mm isotropic resolution, suitable for registration to a standard template in an FMRI protocol".
 
 It may additionally be useful to disambiguate any abbreviations in the name of the sequence, for example "bold_mbep2d_MB4P2_task_faces" could be described as "multiband 2D echoplanar sequence; multiband acceleration factor 4, PAT (GRAPPA) factor 2; for faces task.".
 
@@ -143,7 +143,7 @@ For fieldmap sequences, it may be useful to say which BOLD sequence they will be
 Where a specific task is mentioned, you could link to where that task is shared, or published analysis of any data using that task.
 
 ## 6. Save
-Once all required fields have been completed, you will be able to save the entry to the protocols database. Press "Save" to progress to return to the list of your protocols
+Once all required fields have been completed, you will be able to save the entry to the protocols database. Press `Save` to progress to return to the list of your protocols
 
 
 ## 7. Set visibility