protocols_guide_internal-how-1.md

layout: default
title: Add a new protocol
grand_parent: Open MR Protocols
parent: WIN Members
has_children: false
nav_order: 3

Adding a new protocol entry to the database

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Contents

• 1. Prepare the required files
• 2. Upload
• 3. Top level protocol information
• 4. Attachments
• 5. Sequence level protocol information
• 6. Save
• 7. Set visibility
• 8. Reference List

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.

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.

1.3 Redact confidential information from the scanning procedure and convert it to a pdf.

Any names should be redacted from the scanning procedure unless permission to be listed has been provided by those individuals. Review the complete scanning procedure document (including instructions such as "check voxel location with ") and redact all identifiable information which you do not have permission to share. These details can be replaced with the word "REDACTED" or covered with a black rectangle.

Review all images and ensure that identifiable information such as participant IDs are redacted (cover with a black rectangle). Ensure identifiable facial features (in sagital views of slice pack positioning) are redacted (cover with a black rectangle).

Currently, only the owner of the project is able to edit the uploaded protocol. If you would like to suggest changes to someone else's protocol you can do so by emailing the admin team who can then contact the project's owner.

You might want to add a statement such as "available for re-use, but I'm unable to assist with implementation" in the usage notes to clarify the extent of assistance you are able to provide.

2. Upload

2.1 Log in to the database.

Only WIN members (as determined by SSO authentication) are able to deposit protocols in the database.

To log in:

1. Go to 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.

2.2 Add a new protocol entry

Protocols are saved to individual user profiles.

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.

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.

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 below).

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.

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.

Start typing keywords to select from a built in list. Consider adding keywords relating to:

1. The sequence type (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

3.3 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.

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 below).
3. Your terms for reuse (see Issuing a doi and licence 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.

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).

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

If you are publishing protocol which uses a custom pulse sequence, please make it clear whether you are happy to also share the sequence.

If you are happy to share the sequence, please include the following guideance:

"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.
• 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.

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 you are not able to share the custom 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."

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.

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.

Each of the sections below should be completed for each sequence.

5.1 Sequence name

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.

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 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.".

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.

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.

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.

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 confirm WIN 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 below).

If you identify a protocol as open access, this will trigger a review by database administrators. Further detail of the review process coming soon.

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.

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.

We recommend that you consider using the CRediT system for identifying individual author contributions. You may wish to order authors alphabetically.