This document describes how to enter and update subject visits in a project governed by a defined protocol. To follow along with the examples shown below you may want to create an identical protocol following the directions in the link below or import this Example_Protocol.json file we built there and assign it to a test project you can work with if you are an XNAT administrator or project owner. If you are not, that step will need to be done for you by an administrator or project owner or consult the Tutorial Setup section below.
To learn how to create protocol definitions as a project owner or administrator, click here.
Most of the following setup might be performed by an XNAT system admin, or project owner. In a subject visit data entry role, you would not need to perform the following steps:
If you don't already have a throw-away project in XNAT you can tinker with, I suggest creating one for use in getting acquainted with the features of the Visits & Protocols plugin. For help with this, see Creating and Managing Projects.
Your test project as the project owner will then need the protocol mentioned above assigned to it. Go to the project page and click on the protocol tab. Select the appropriate protocol and version number from the dropdowns and click "Set Protocol".
Step-by-step guide to recording subject visits
To begin, you will want to create a sample subject by clicking on New -> Subject from the XNAT Menu bar.
If you need help creating a new subject, see Creating and Managing Subjects.
- Subject visits on a project with an associated protocol are managed on the Protocol Schedule of the Subject page which now looks a little different from the standard XNAT subject page.
Note that at any point you can click on the "View As Experiment List" toolbar button under the Protocol Schedule heading to switch back to the default view which is, just a simple list of the experiments, scans and assessors that have been completed for this subject.
Otherwise you will notice that the subject's first expected baseline visit detailing the protocol's expected experiments for this first visit is waiting to be "opened".
Additionally, if "unexpected visits" have been enabled on your protocol, you'll have the option to create an "Ad Hoc" visit in the toolbar as seen above. We'll cover more on this later.
- For now, let's open this subject's first visit. Click "Open Visit".
Assuming that the subject is brand new and that they are just showing up for their first visit, the current date will appear by default in the dialog's "Visit Date" field, but this can be changed by clicking the calendar icon and selecting a different date if for instance it makes more sense for your project to enter this data at a later point in time. Click "Open Visit" on the dialog to continue.
- We now have our first empty visit ...and a preview of the upcoming expected second visit with the dashed border and you will notice if you attempt to open that one imdeiately on a our project with a protocol that doesn't allow multiple open visits, it won’t let you until the first one is closed.
- Now you just need to satisfy the required experiment by creating them or uploading images as you normally would in XNAT.
There are equivalently three ways to do this... You can:
- Upload an image session. The project and subject you had been working with should be pre-populated in the first two dropdowns of the visit entry page. Additionally, you'll notice the "Visit" field in which you specify the appropriate visit to assign the session to upon successfully uploading it.
- Add a new experiment / imaging session of the specified data type. Similarly, you'll notice the "Visit" field in which you specify the appropriate visit to assign the experiment to upon successfully creating it.
- Move an existing experiment for the subject to the currently open visit(s). In the case where a subject may already have experiments completed, they will show up under the "Unsorted Experiments" section of the protocol schedule on the subject visits page. If there are valid visits open that they can be assigned to, a dropdown will be displayed in the last "Move to Visit" column. Select the appropriate visit to move it to (there will likely only be one unless your protocol allows for multiple open visits) and you will have completed that particular visit requirement, or added it as an optional experiment (if the protocol allows for "unexpected visits").
- Once we've satified the experiment requirements, we're allowed to close the visit. Click the "Close Visit" button in the upper right corner. Once you've closed the visit, it cannot be edited or deleted unless you "Reopen" it.
- At this point, we're done with that visit.
Let's say four months rolls around and the subject comes back in for their second visit. We open the second visit...
But for some technical reason no data can be collected for the second CT scan required above. If our protocol allows for "deviations", we'll have to enter an explanation for one in this case.
- With the MR and it's associated assessor requirements satisfied, plus the deviation for the CT session, this visit can also now be closed.
- ...and the Final visit can be opened
- Note that this will be designated a “Terminal Visit” and further data collection for this subject under the protocol will cease.
- Another scenario in which you might enter a “Terminal Visit” is if a subject drops out of the study for other reasons or dies. In this case you would click the "Create a Terminal Visit" toolbar button, or "Create Ad Hoc Visit" and check the "Make this a terminal visit" checkbox if "Ad Hoc Visit" allowances are enabled on your protocol as they are in the example below.
- Again, the protocol schedule for this subject ends immediately at this point.
This concludes the subject visit data entry tutorial.