1. Entering cognitive data

2. fMRI data

3. Surgical conference data

4. Electrical Stimulation Mapping (ESM) and ISA (Wada) data

5. Surgery data

The flow chart for data entry into NED is as follows.

Data entry: Cognitive data

• Forms used: (1-10+) Neuropsych test forms

• Required: (1) folder holding outputs (.txt) from neuropsych test scoring program; (2) folders holding reports (.docx) and paired neuropsych summary sheets (.xlsx), (3) redcap bash scripts.

• Data entry mode: use data import to upload data files (.csv files)

At the end of test session(s) the neuropsychologist enters these scores into (1) scoring software, which produces a table of scores (.txt) and (2) a manually compiled summary for review, interpretation, and report writing in patient care (.xlsx).

When data is to be entered:

1. A bash shell script is run on the group of .csv files from the neuropsych scoring software to convert the data into NED redcap format. This takes as input a .csv file holding one or more patients’ data. There is little manipulation of the data, here: headings (redcap columns – e.g., the record and session IDs) are added for each patient (each row in the .csv).

   Specifically: Check the script 1_bash to make sure it is taking the right folders as input. Then run it. A folder ‘redcap’ is created on the desktop.

2. Check the errors that are generated at run time - check for any duplicates. Similarly, errors are written to text files in the folder “redcap/errors.” Correct the errors in the raw data (and scoring software) and rerun.

3. Upload the file redcap/upload/cognitive.csv into redcap.

In detail –

Prepare raw data

• Excel summary sheets:

  • Confirm all patient folders are within a single folder, with each structured as:

    last_first_YYYYMMDD [folder]

    last_first_YYYYMMDD_report.docx [report]
    last_first_YYYYMMDD_scores.xlsx [summary]

  • Avoid including any commas in the .xlsx.

• Cognitive testing software: Export data

  • Be sure to adjust the date range to only cover interim.

  • Demographic exports: Choose full demographic (not edu).

  • HRB: Highlight and select all for export, but also adjust date range.

  • Filenames must end as follows:

    • ACS TOPF: *topf.txt

    • ACS Effort: *effort.txt

    • WAIS4: *wais.txt

    • WMS4: *wms.txt

    • WAIS4-dem. cor.: *wais-dc.txt

    • WMS4-dem. cor: *wms-dc.txt

    • WMS4-additional: *wms-adl.txt

    • HRB: *hrb.txt

  • Not added currently:

    • WAIS4-additional: *wais_adl.txt

Quality check

• Before uploading:

  • Check the error files in the errors folder. Correct in both the files, and the scoring software.

  • Check the ‘duplicates’ errors at runtime. Also correct.

  • In particular: Look for errors in the session date that may inadvertently occur when test data is entered on a different day to the testing session.

• When uploading:

  • Look at the errors redcap picks up, and correct these.

• Put all files for upload into the data archive for posterity.

• Note in the notes field that it has been quality checked.

Data entry: fMRI

• Forms used: (1) fMRI, (2) demographics.

• Required: Nil.

• Data entry mode: web interface.

Functional MRI referrals are forwarded by the team. These need to be recorded, patients awaiting scheduling and scanning to be tracked, and then the acquisition and analysis of the data summarized. The data is stored (of course) outside NED in a folder following (anonymous) BIDS conventions, on a separate HIPAA-compliant server share to NED.

• When patients are referred, NED is accessed via the web interface and the patient’s record_id is entered. The demographics form is filled out, then the fMRI form.

Scheduling fMRI patients

• Open the redcap web interface and identify outstanding patients using the report ‘fMRI: to be scheduled’, or a specific patient via the ‘add/edit record’ function.

• Click relevant cases to review details.

• Document the steps of each contact here.

Scanning fMRI patients

• Open the redcap web interface and identify the patient using the ‘add/edit record’ function.

• Document problems at scan time in the notes section.

Analysis

• Open the redcap web interface and identify the patient using the ‘add/edit record’ function.

• Note the results in the relevant fields, and upload copies of the report and images.

Data entry: Surgical conference/summary

• Forms used: (1) summary

• Data entry mode: web interface

Key clinical data are stored in the data summary form, and (from the patient side) the history form. The focus is on key information required for decision making.

• When a patient is discussed at conference, the data are entered directly via the web interface.

• Data are also entered separately via the web interface when a case is summarized, e.g. in clinic.

Data entry: Intracranial and ISA reports and data

Forms used: (1) summary

• Data entry mode: web interface

Fields allowing upload of key relevant data - pptx, maps, results tables - are included in the summary sheet.

For intracranial language mapping, the resulting data include images (jpgs or pptx) of the electrode placement; of the mapping results (jpgs or pptx); and a summary of the results of contacts being stimulated (xlsx).

Data entry: Surgery scheduled or completed

• Forms used: (1) surgery and (ideally) (2) demographics

• Data entry mode: web interface

When patients are scheduled for surgery and the team is notified, this data needs to be entered.

• When patients are referred, the patient’s record ID is entered into the web interface along with key details on the planned surgery by a team member.

• When patients have completed surgery, the surgery details are updated in the web interface (team member).

Additionally, please email me so that we can schedule (A) final pre-operative neuropsych if necessary to ensure all required clinical tasks are up to date and (B) one year post-operative evaluation for ongoing care.

surveys

• Must have form that holds email. It must be the first form in the database (to make things simple).

• Turn on survey option in the main page.

Data entry: History forms

• Forms used: (1) demographics. Then

  • (2) history > (3) edi-sf > (4) nddie and

  • (5) MRI screen

• Data entry mode: forward email to participant, who then completes via web interface.

When a patient is scheduled, forward them a link to both the history form and the MRI screen, and ask them to complete both. This is achieved by:

• Complete the demographics form, and include the email (essential).

• In the main window, select ‘Survey Distribution Tools’ (on left).

• Select ‘Compose Survey Invitations’. Select the participant (on the left) and then review and edit he ‘compose’ text. This is the email that will be sent. You can select to set a reminder, too, if need be.