Merge branch 'mtach-master-patch-17006' into 'master'

Update docs/protocols/protocols_guide_internal-how-1.md

See merge request !16

docs/protocols/protocols_guide_internal-how-1.md

@@ -30,7 +30,7 @@ nav_order: 2
 ## 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 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.
+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 and providing 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.
@@ -77,61 +77,59 @@ Protocols are saved to individual user profiles.
 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.
+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 to understand your decisions and/or implement your protocol.
 
-NOTE: If you are publishing custom pulse sequences, please be sure to indicate your willingness and requirements for shring the pulse sequence (see [3.4.1 Custom Sequences](#3-4-1-custom-sequences) below).
+NOTE: If you are publishing customised pulse sequences, please be sure to indicate your willingness and requirements for sharing them (see [3.4.1 Custom Sequences](#3-4-1-custom-sequences) below).
 
 ![gif - top details](../../../img/img-protocols/gif_top-details.gif)
 
 ### 3.1 Project, hardware and species
-Some fields of this section are identified by the database from your pdf. Others have to be selected by you. Complete the following selections by selecting the appropriate item from the dropdown menus.
+Some fields of this section are autmatically retrieved from your pdf and other ones have to be added by selecting the appropriate items from the dropdown menus like:
 1. Project (select from Calpendo registered projects)
 2. Scanner
 3. Species
 4. Post mortem (tick if appropriate)
 
 ### 3.2 Keywords
-Keywords can be used by users to find your protocol. Note that when users are searching for a protocol, their search query will be matched to keywords only, not text in the body of the entry.
+Keywords can be used by other researchers to find your protocol. Note that their search query will be matched to keywords only and not to the text in the body of the entry.
 
-Start typing keywords to select from a built in list. Consider adding keywords relating to:
-1. The sequence type (e.g., "T1 structural")
+Start typing keywords to select from a built-in list. Consider adding keywords related to:
+1. Type of sequences (e.g., "T1 structural")
 2. Regions of interest
-3. The participant population or clinical condition
-4. Cognitive or behavioural function
-5. Task or stimulus properties
+3. Participants or clinical conditions
+4. Cognitive or behavioural functions
+5. Tasks or stimuli properties
 
 
 ### 3.3 Description
-This section should identify and highlight important features of the protocol. For example the study design, methods, and procedure. The Radiographers procedure abstract is sufficient.
+This section should identify and highlight important features of the protocol like the study design, the methods, and the procedure. The abstract of radiographers' procedure should be sufficient.
 
 
 ### 3.4 Usage guidance
-This section should provide high-level instructions for use of this protocol. Where possible, we recommend including the following:
-1. **Contact details** for anyone looking to discuss re-use of the project. Note this information will be publicly available if your protocol is made public. Only include contact details where explicit permission has been granted.
-2. **How to cite** this entry, including any references you would like to be cited in addition to this entry (see [Issuing a doi and licence](#issuing-a-doi-and-license) below).
-3. **Your terms for reuse** (see [Issuing a doi and licence](#issuing-a-doi-and-license) below), including any specific terms around authorship before others reuse this protocol. For example, "We request that future users of this protocol contact the authors of this entry to discuss collaboration and authorship agreements relating to reuse." This may be particularly relevant for experimental protocols or sequences.
+This section should provide high-level instructions for the use of this protocol. Where possible, we recommend including the following:
+1. **Contact details** for anyone willing to discuss the re-use of the protocol. Note this information will be publicly available if your protocol is made public. Only include contact details where explicit permissions have been granted.
+2. **How to cite** this entry including any references you would like to be cited in addition to this entry (see [Issuing a doi and licence](#issuing-a-doi-and-license) below).
+3. **Your terms for reuse** (see [Issuing a doi and licence](#issuing-a-doi-and-license) below) including any specific terms around authorship before re-using this protocol for example: "We request that future users of this protocol contact the authors to discuss collaboration and authorship agreements related to the reuse". This may be particularly relevant for experimental protocols or sequences.
 
-You may also like to include some practical guidance, such as the total length of the scanning session, staffing levels, or any peripheral equipment. You may refer the reader to the radiographers procedure file if this is to be attached (see [4. Attachments](#4-attachments)).
+You may also like to include some practical guidance such as the total length of the scanning session, the staffing levels, or any peripheral equipment. You may refer the reader to the radiographers procedure file if this has been attached (see [4. Attachments](#4-attachments)).
 
-You should also highlight non-standard software or sequence requirements, such as custom pulse sequences (see [3.4.1 Custom Sequences](#3-4-1-custom-sequences)).
+You should also highlight non-standard software or sequence requirements such as customised pulse sequences (see [3.4.1 Custom Sequences](#3-4-1-custom-sequences)).
 
-### 3.4.1 Custom Sequences
-If you are publishing protocol which uses a custom pulse sequence, please make it clear whether you are happy to also share the sequence.
+### 3.4.1 Customised Sequences
+If you are publishing a protocol that uses a customised pulse sequence, please make it clear if you are happy to share it. If so, please include the following guideance:
 
-If you are happy to share the sequence, please include the following guideance:
+"This protocol uses a customised pulse sequence and its author is willing to share it with other labs provided:
 
-"This protocol uses a user written custom pulse sequence.  The author of the pulse sequence is willing to share it with other labs provided:
-
-- The lab/hospital has the appropriate contracts in place with Siemens and idea licence that allow custom pulse sequences to be installed on their system.
+- The lab/hospital has the appropriate contracts and licences with the scanner's vendor that allow customised pulse sequences to be installed on their system.
 - We have a version that is available for your platform [(e.g. we currently can only supply for VB11C and VB11E)]
-- You are willing to arrange with Siemens for a C2P agreement for this sequence
-- You are willing to arrange for a sequence transfer agreement between Oxford University and your institution to be signed.
+- You are willing to arrange for a C2P agreement with Siemens for this sequence
+- You are willing to arrange for a sequence transfer agreement between Oxford University and the interested institution to be signed.
 
-If all of the above apply then please contact [email address if the PI] in the first instance.  Please note that neither Siemens nor Oxford University make no commitment to support this transfer."
+If all of the above apply then please contact [email address if the PI] in the first instance.  Please note that neither Siemens nor University of Oxford makes no commitment to support this transfer".
 
-If you are not able to share the custom sequence, please include the following guidance:
+If you are not able to share the customised sequence, please include the following guidance:
 
-"This protocol uses a user written custom pulse sequence.  We do not have the resources to share the sequence with other labs, so the protocol is provided for your information only."
+"This protocol uses a customised pulse sequence.  We do not have the resources to share the sequence with other labs, so the protocol is only provided for your information."
 
 ## 4. Attachments
 Browse to and add any attachments to support the implementation of your protocol. This should ideally include the (redacted) radiographers procedure. You may additionally choose to attach analysis of pilot data, for example.
@@ -139,7 +137,7 @@ 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. 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.
+You can add details specific to individual sequences. These details may make the understanding of the outputs easier for other users. You can include information about why these sequences where chosen or refer to decisions made during piloting. 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.
 
@@ -149,37 +147,37 @@ 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
-Keywords including for example modality, ROIs, clinical conditions, study population, study type.
+Keywords including for example modality, ROIs, clinical conditions, type of study and population.
 
 ### 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".
+It provides key features that might help someone to decide whether the sequence meets their needs or not. For example, “A standard T1-weighted structural scan of 1mm isotropic resolution is 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.".
+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 echo-planar sequence; multiband acceleration factor 4; PAT (GRAPPA) factor 2; for faces task.".
 
 For fieldmap sequences, it may be useful to say which BOLD sequence they will be used to correct.
 
-Where a specific task is mentioned, you could link to where that task is shared, or published analysis of any data using that task.
+Where a specific task is mentioned, you could add the link to where that task is shared or published analysis of any data using that task.
 
-Consider adding specific purpose and pros/cons of the sequence. For example, one sequence has a high temporal resolution but relatively low spatial resoltuion. Or one sequence is developed to focus on a specific brain area. Cons may include dropout or poor signals from certain regions.
+Consider adding specific purpose and pros/cons of the sequence. For example, one sequence has a high temporal resolution but relatively low spatial resoltuion or it has been developed to focus on a specific brain area. Cons may include dropout or poor signal from certain regions.
 
 ## 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 and return to the list of your protocols.
 
 
 ## 7. Set visibility
-By default, your entries will be set to `Internal (University Only)` visible when you add them to the database. This means users will be required to log into the the protocols database with an SSO in order to review or download your entry.
+By default, your entries will be set to `Internal (University Only)` visibility when you add them to the database. This means users will be required to log into the the protocols database with an SSO in order to review or download your entry.
 
 After they have been entered onto the database you can make individual protocols publicly visible (`Open Access`) and identify them as `WIN Recommended` protocols as appropriate.
 
 ### Open Access Actions
 If you choose to make a protocol public ("open access") ensure you have added a license note to your entry, reserved a doi for the protocol using zenodo, and added the doi to the usage guidance (see [Issuing a doi and licence](#issuing-a-doi-and-license) below).
 
-If you identify a protocol as open access, this will trigger a review by database administrators. <mark>Further detail of the review process coming soon. </mark>
+If you identify a protocol as open access, this will trigger a review by the database's administrators. <mark>Further details of the review process coming soon. </mark>
 
 ## 8. Reference List
-This field features prominently at the top of the entry when it is accessed by users, so it may be appropriate to repeat any important citation information which is listed in the usage guidance.
+This field features prominently at the top of the entry when it is accessed by users, so it may be appropriate to repeat any important citation details which are listed in the usage guidance.
 
-Add any references which are relevant to this protocol, for example the paper or pre-print which it accompanies. You can also use this space to draft the author list and track changes in contribution.
+Add any references which are relevant to this protocol for example the accompanying paper or pre-print. You can also use this space to draft the author list and track changes in contribution.
 
 We recommend that you consider using the [CRediT](https://casrai.org/credit/) system for identifying individual author contributions. You may wish to order authors alphabetically.