##### 1.1 Ask your radiographer for your protocol pdf and scanning procedure file.
### 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.
##### 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.
### 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.
### 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 <NAME>") 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).
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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. Upload
##### 2.1 Log in to the database.
### 2.1 Log in to the database.
Only WIN members (as determined by SSO authentication) are able to deposit protocols in the database.
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##### 2.2 Add a new protocol entry
### 2.2 Add a new protocol entry
Protocols are saved to individual user profiles.
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##### 2.3 File type error
### 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
## 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.
##### 3.1 Project, hardware and species
### 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
### 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:
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5. Task or stimulus properties
##### 3.3 Description
### 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
### 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)
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You should also highlight non-standard software or sequence requirements, such as custom pulse sequences.
#### 4. Attachments
## 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 chose 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
## 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.
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
### 5.1 Sequence keywords
1. Keywords including for example modality, ROIs, clinical conditions, study population, study type.
##### 5.2 Sequence description
### 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.".
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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
## 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
## 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 <mark>confirm WIN SSO?</mark> 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.
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"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).
#### 8. Reference List
## 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.
