Coordinate systems

Author: Francois Tadel

This page describes the various coordinate systems used in Brainstorm, and explains how to convert beetween referentials.

Subject Coordinate System (SCS / CTF)

Brainstorm uses the CTF head coordinate system. All the surfaces, sensors and additional points are converted into this system when they are imported in Brainstorm.

It is defined in the following way:

scs_axes.png





The affine transformation from MRI to SCS coordinates is saved in the MRI SCS structure:

Nasion (NAS)

The nasion is the intersection of the frontal and two nasal bones of the human skull. Its manifestation on the visible surface of the face is a distinctly depressed area directly between the eyes, just superior to the bridge of the nose (source: Wikipedia).

Use the coronal orientation to define it.

NAS.gif

Pre-auricular points (LPA, RPA)

preauricular.gif

The proper definition of the preauricular point is: "a point of the posterior root of the zygomatic arch lying immediately in front of the upper end of the tragus". This is illustrated with the green point below. The problem with this definition is that it can be really difficult to localize precisely on the MRI. It can lead to severe misregistration between MRI and MEG/EEG. More information on the anatomical location of this point on the FieldTrip website.

Our proposition is to use instead the junction between the tragus and the helix, marked with a red dot in this figure. It can be located much more precisely both anatomically and on the MRI slices.

You can choose to use this definition of the "preauricular point" or not.

Use the sagittal orientation to define it.

LPA.gif


The most important is to use the same fiducial convention for all the steps: digitization of head points (eg. Polhemus) and analysis with Brainstorm.

Notes for CTF users

Using a CTF system, you would probably prefer to use the head localization coils to indicate these NAS/LPA/RPA points, instead of these "anatomically correct" points. The coordinate system in the CTF files is based on the position of the three coils you stick on the head of the subject. Typically, the nose coil is slightly above the nasion, and the ear coils about one centimeter more frontal than the points that were previously described.

A good practice is to take pictures of the subject with the coils on, right before bringing him/her in the MEG, and digitize the position of the center of the coils as the nasion/LPA/RPA. Then, when importing the MRI in Brainstorm, try marking as accurately as possible the position of the coils in the MRI. You cannot be very precise at this point, but the errors here are fixed later with the automatic registration.

LPA.gif

IMPORTANT: These comments do not apply if you use the Brainstorm Digitize program to drive the Polhemus device. In this case, you are asked to digitize two sets of NAS/LPA/RPA points: the coils and the real anatomical points. Just make a copy of the .pos file saved by Digitize in the .ds folder, then set the real anatomical points in the MRI. Brainstorm is going to automatically handle the transformation between the CTF coils coordinate system and the real subject coordinate system. The result is usually much more accurate and does not require to take pictures of the subjects.

Using a default anatomy

The fiducial points (Nasion, LPA, RPA) used in your recordings might not be the same as the ones used in the anatomy templates in Brainstorm (ICBM152, Colin27, FSAverage). By default, the LPA/RPA points are defined at the junction between the tragus and the helix, as represented with the red dot. If you want to use an anatomy template but you are using a different convention when digitizing the position of these points, you have to modify the default positions of the template with the MRI Viewer.

MRI coordinates

Coordinates system used in the space of the MRI volume, in millimeters:

World coordinates

Coordinates system used in the original MRI file, that was loaded as the reference MRI for a subject. It is defined by a 4x4 matrix saved directly in the MRI file. From NIfTI .nii files, it uses the matrix sform if available, or otherwise the matrix qform (see the NIfTI documentation). From FreeSurfer .mgh/.mgz files, it uses the vox2ras matrix (see the FreeSurfer documentation).

In practical terms, it corresponds to the coordinates you see in the title bar when loading your volume in MRIcron, while the coordinates you see in the text boxes correspond in Brainstorm vocabulary to "voxel coordinates". For subject data, it corresponds most of the time to scanner coordinates. For atlases, it may correspond to normalized coordinates (e.g. MNI coordinates).

If available, the transformation from voxels to world coordinates is saved in the field InitTransf{'vox2ras'} of the MRI structure.

MNI coordinates

In order to compare the anatomy of multiple human brains or compute group statistics, it is necessary to define a common reference system. Two types of normalized systems have been widely used in the literature in the past: the atlas defined by Jean Talairach, and the MNI stereotaxic coordinates. You can read about the differences between these two systems here.

While the Talaraich system has been progressively abandonned, the "MNI space" has been increasingly used, thanks to the development of automatic normalization methods in open-source neuroimaging software. Successive updates to the reference brain and software versions led to the coexistence of multiple "MNI spaces". For an exhaustive list, refer to these two websites: BIDS specification, Lead-DBS.

In Brainstorm, MNI coordinates refer to the normalized space defined in SPM12, also referred to as IXI549 space. Like the MRI coordinates above, it is in mm, and the (X, Y, Z) axes are oriented towards (right, anterior, dorsal). The origin is at the AC point (see Talairach section below) of the template, with the (negative) Y axis also going through the PC point of the template.

Computing this MNI normalization for a subject does not alter the input MRI or create a new normalized volume: it only stores a transformation that allows referencing the subject's MRI volume with standardized MNI coordinates. There are two options: a linear and a non-linear approach.

mni_norm.gif

Linear normalization

Non-linear normalization

References

MacOS troubleshooting

Error "mexmaci64 cannot be opened because the developer cannot be verified":

ACPC coordinates

This coordinate system is recommended for iEEG coordinates in the BIDS specification. It relies on two points, the anterior and posterior commissures (AC and PC), and the midsagittal plane. The third point needed here, the interhemispheric point (IH), is used to define this plane. The anatomical landmarks are determined in the individual's anatomical scan and no scaling or deformations have been applied to the individual's anatomical scan.

References:

Anterior commissure (AC)

Description of the anterior commissure at this Wikipedia page.

Technique to localize it:

AC.gif

Posterior commissure (PC)

Description of the posterior commissure at this Wikipedia page.

Technique to localize it:

PC.gif

Interhemispheric point (IH)

Pick any point in the interhemispheric space, somewhere in the top of the head. Do not use a point too close from the commissures.

IH.gif

Talairach coordinates

Similar to the ACPC coordinates, but with an additional piecewise scaling to match the Talairach-Tournoux (1988) atlas. See FieldTrip documentation. No used in Brainstorm.

CapTrak coordinates

This coordinate system is accepted for EEG coordinates in the BIDS specification. It relies on the three head points LPA/RPA/NAS described above.

References:

Neuromag coordinates

This coordinates system is not used in Brainstorm, and described here only FYI. All the information contained in Neuromag .FIF files are in this CS, and converted to Brainstorm SCS at importation.

It is defined in the following way:

Converting between coordinate systems

The conversions between coordinate systems is handled with one single function cs_convert:

Pdest = cs_convert(sMri, 'src', 'dest', Psrc);

Examples:

P_mri = cs_convert(sMri, 'voxel', 'mri', P_voxel);   % Voxel => MRI coordinates
P_mni = cs_convert(sMri, 'scs', 'mni', P_scs);       % SCS   => MNI coordinates

Brainstorm .pos files

The .pos files generated with the Brainstorm Digitizer contain both the positions of the anatomical landmarks (nasion, left ear, right ear) and the position of the head localization coils (HPI).

Having the two sets of points allows us to convert automatically from the native CTF coordinates (based on the coils) to the recommended landmarks in Brainstorm (based on the anatomical landmarks). When a Brainstorm .pos file is present in the CTF .ds folder, it is loaded automatically and used to convert the positions of the EEG and MEG sensors to the anatomical reference. This is done automatically without any message or user confirmation. In this case, you should mark the anatomical landmarks (real nasion and tragus/helix junctions) in the MRI Viewer when importing the anatomy. This is what is described in the introduction tutorials.

Otherwise, if you are importing CTF recordings without a Brainstorm .pos file in the .ds folders, or if you are importing the .pos files after linking the recordings to the database, you should typically select the positions of the CTF HPI coils in the MRI viewer.

The syntax of these .pos files is the following, one line per digitized point:

Number of EEG electrodes
Index   Label   X   Y   Z     : Defines an EEG electrode
Index           X   Y   Z     : Defines a head shape point
Label           X   Y   Z     : Defines a reference point

In the .pos files, the anatomical landmarks are labelled Nasion/LPA/RPA, and the CTF HPI coils are labelled HPI-N/HPI-L/HPI-R (for nasion coil, left coil, right coil). Note that in the CTF software, the HPI coils are labelled NAS/LPA/RPA, which can lead to some confusion.

We usually take multiple measures of each reference point and average them when we load the file. This helps improving the accuracy of the registration.

2
1       Cz       5.29886357      -0.39211620      13.97175211
2       Pz      -2.72999896       0.56457819      14.80592908
3                9.47286768       0.09984190      -2.22056385
4                9.61745050      -0.00705346      -2.64471836
[...]
242              2.68917264       3.02778502      13.88281027
243              1.10525214       3.54043941      14.17347208
Nasion   9.59228188      0.08328658     -1.88504105
LPA     -0.47469294      6.81987024      0.62870235
RPA     -0.96029260     -6.72333418      0.16475241
Nasion   9.76823213     -0.11917776     -1.87417223
LPA     -0.29274026      6.88415084      0.70120923
RPA     -0.99183277     -6.70128616      0.08443862
HPI-N   10.61990713      0.01532629      0.00407281
HPI-L    0.20165313      6.74350937     -0.00134360
HPI-R   -0.23124566     -6.76723759     -0.00008921
HPI-N   10.61095674     -0.01532629     -0.00407281
HPI-L    0.27017080      6.81335558      0.00134360
HPI-R   -0.24057827     -6.78962736      0.00008921

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CoordinateSystems (last edited 2024-03-01 14:39:00 by RaymundoCassani)