This page will teach you how to run an assessment of the accuracy of your HPI-digitization before entering the MSR

### Why?

There are two main reasons why you would want to do this

1. This allows you to do a rough check of whether you have moved the Polhemus on the forehead during digitization, which can seriously disturb your co-registration of MEG and MRI data
2. It can save you a lot of time compared to only realizing it before you have to start your recording, where you would also cause discomfort to your subject by needing to the get them out of the scanner and do the digitization over again

### How?

Follow these simple steps: (be sure to run any commands exactly as shown):

1. When digitizing the subject do fiducials and HPI-coils in the usual manner
2. When digitizing extra points (head shape), digitize the HPI-coils again in the same order as before, so that they will be the four first extra points
3. Before finishing extra points, (head shape), digitize the HPI-coils again in the same order as before, so that they will be the four last extra points
4. Save preparation on the remote desktop and load it on DACQ (the acquisition desktop)
5. With the subject still in the digitization chair, make a short recording (~ 10 s) (omit HPI-coils) and save it (preferably as “dig_test”)
6. Run the semi-automated script (see below) for assessing the discrepancy between digitized HPI-coil positions and the first four points and between digitized HPI-coil positions and the last four points
7. If calculated distance is greater than 2 mm, we suggest that you do redo the digitization

### Running the script

1. Open a terminal (there’s a shortcut on the desktop of DACQ)
2. Enter the following command into the terminal (write exactly what it says):
./scripts/assess_hpi_digitization.sh
1. You will now be prompted to enter your project, subject, date and filename of the just saved recording (default: dig_test.fif) (example shown below (colouring not relevant))
This script will allow you to check the accuracy of your digitization
This requires that you have digitized the HPI-coils again as the FIRST four ponts in your head shape digitization AND as the LAST four points in your head shape digitization

Press <ENTER> to continue!

## Default: current project chosen in Acqusition
Type in PROJECT name, EXACTLY as it is called in </neuro/data/sinuhe>
creating_a_black_hole

## Default: current subject chosen in Acqusition. It is possible to put in just the number, e.g. 0177
Type in SUBJECT name (format <NatMEG_****>, where **** is a 4-digit number
stephen_hawking

## Default: today's date
Type in DATE (format "YYMMDD", e.g. 160613 for June 13th 2016 ## if nothing is entered, today's date will be used as input
201231

## Default: dig_test.fif
Type in FILENAME of digitization test, default "dig_test.fif" ## if nothing is entered, "dig_test.fif" will be used as input
dig_test.fif

Press <ENTER> to start calculation!

### Output

Here’s some example output (again colouring is not relevant):

IGNORE THIS WARNING
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
This filename (/data/neuro-data/spatial_precision/MEG/NatMEG_0177/160613/dig_tes
t.fif) does not conform to MNE naming conventions. All raw files should end with
raw.fif, raw_sss.fif, raw_tsss.fif, raw.fif.gz, raw_sss.fif.gz or raw_tsss.fif.
gz
This file contains raw Internal Active Shielding data. It may be distorted. Elek
ta recommends it be run through MaxFilter to produce reliable results. Consider
closing the file and running MaxFilter on the data.
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
IGNORE THIS WARNING

DISTANCE BETEWEEN HPI AND FIRST FOUR CONTROL POINTS
-----------------------------------------------------------------------------
Distance between HPI-digitization no. 1 and control point no. 1 is: -33 mm
Distance between HPI-digitization no. 2 and control point no. 2 is: -0.8 mm
Distance between HPI-digitization no. 3 and control point no. 3 is: -23.8 mm
Distance between HPI-digitization no. 4 and control point no. 4 is: 19.2 mm

DISTANCE BETEWEEN HPI AND LAST FOUR CONTROL POINTS
-----------------------------------------------------------------------------
Distance between HPI-digitization no. 1 and control point no. 1 is: -66.8 mm
Distance between HPI-digitization no. 2 and control point no. 2 is: -14.5 mm
Distance between HPI-digitization no. 3 and control point no. 3 is: 20.4 mm
Distance between HPI-digitization no. 4 and control point no. 4 is: 204.6 mm


This suggests some pretty serious errors, (maybe the Polhemus on the forehead was moved or a black hole was created) and you should redo the digitization