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[ENH, MRG] Add scanner RAS coordinate frame definition #444

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Sep 7, 2021
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[ENH, MRG] Add scanner RAS coordinate frame definition #444

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dab5475
add scanner RAS
alexrockhill Aug 31, 2021
9438816
clarify that freesurfer and scanner RAS origins are generally different
alexrockhill Sep 1, 2021
2d2b42e
mention the relation of scanras to dicom and nifti
robertoostenveld Sep 7, 2021
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49 changes: 32 additions & 17 deletions faq/how_are_the_different_head_and_mri_coordinate_systems_defined.md
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Expand Up @@ -32,23 +32,24 @@ Imaging methods such as MRI and CT result in 3-D volumetric representations of t

| system | units | orientation | origin | scaling | notes |
| ------------------ | ----- | ----------- | ------------------------------------------- | --------------------------------------------------------------------------------------------------------- | ---------------------------- |
| ACPC | mm | RAS | anterior commissure | native, i.e., not normalized to a template | |
| Allen Institute | mm | RAS | Bregma point | | |
| Analyze | mm | LAS | | native | |
| BTi/4D | m | ALS | between the ears | native | |
| CTF MRI | mm | ALS | between the ears | native | voxel order can be arbitrary |
| CTF gradiometer | cm | ALS | between the ears | native | |
| CapTrak | mm | RAS | approximately between the ears | | |
| Chieti ITAB | mm | RAS | between the ears | native | |
| DICOM | mm | LPS | | native | |
| EEGLAB | mm | ALS | between the ears | native | |
| FreeSurfer | mm | RAS | center of isotropic 1 mm 256x256x256 volume | | |
| MNI | mm | RAS | anterior commissure | scaled to match averaged template | |
| NIfTI | mm | RAS | scanner origin (centre of gradient coil) | see [here](https://brainder.org/2012/09/23/the-nifti-file-format/), search for "Orientation information". | |
| Neuromag/Elekta/Megin | m | RAS | between the ears | native | |
| Paxinos-Franklin | mm | RSP | Bregma point | | |
| Talairach-Tournoux | mm | RAS | anterior commissure | scaled to match atlas | |
| Yokogawa | | ALS | center of device | | |
| ACPC | mm | RAS | anterior commissure | native, i.e., not normalized to a template | |
| Allen Institute | mm | RAS | Bregma point | | |
| Analyze | mm | LAS | | native | |
| BTi/4D | m | ALS | between the ears | native | |
| CTF MRI | mm | ALS | between the ears | native | voxel order can be arbitrary |
| CTF gradiometer | cm | ALS | between the ears | native | |
| CapTrak | mm | RAS | approximately between the ears | | |
| Chieti ITAB | mm | RAS | between the ears | native | |
| DICOM | mm | LPS | | native | |
| EEGLAB | mm | ALS | between the ears | native | |
| FreeSurfer | mm | RAS | center of isotropic 1 mm 256x256x256 volume | | |
| MNI | mm | RAS | anterior commissure | scaled to match averaged template | |
| NIfTI | mm | RAS | scanner origin (centre of gradient coil) | see [here](https://brainder.org/2012/09/23/the-nifti-file-format/), search for "Orientation information". | |
| Neuromag/Elekta/Megin | m | RAS | between the ears | native | |
| Paxinos-Franklin | mm | RSP | Bregma point | | |
| Scanner RAS (`scanras`) | mm | RAS | scanner origin | native | |
| Talairach-Tournoux | mm | RAS | anterior commissure | scaled to match atlas | |
| Yokogawa | | ALS | center of device | | |

A/P means anterior/posterior
L/R means left/right
Expand Down Expand Up @@ -252,9 +253,23 @@ The most common definition of the head coordinate system used by the software th
- the Y-axis goes approximately towards LPA, orthogonal to X and in the plane spanned by the fiducials
- the Z-axis goes approximately towards the vertex, orthogonal to X and Y

## Details of the Scanner RAS coordinate system

The **Scanner RAS** coordinate system has the same origin as the DICOM coordinate system, but is rotated 180 degrees around the z-axis. The Scanner RAS coordinate system is identical to the NIfTI scanner coordinate system (qform). It is defined as

- the origin corresponds to the scanner origin, which is the center of the gradient coil
- the x-axis increases from left to right
- the y-axis increases from posterior to anterior
- the z-axis increases from inferior to superior

The process to generate data in this coordinate system can be done for any standard image format (e.g. `.nii`, `nii.gz`, `.mgz`) and is described in more detail in the [Nipy Documentation](https://nipy.org/nibabel/coordinate_systems.html).

Note that the origin of the **Scanner RAS** is defined differently than that of the **Freesurfer** (also known as "Surface RAS" or "TkReg RAS") origin, so they are generally not the same.

## Details of the Talairach-Tournoux coordinate system

The [Co-Planar Stereotaxic Atlas of the Human Brain](https://www.thieme.com/books-main/neurosurgery/product/414-co-planar-stereotaxic-atlas-of-the-human-brain) (1988) by Talairach and Tournoux defines a coordinate system using the Anterior and Posterior Commissure and applies that on a post-mortem dissection of an individual human brain. Furthermore, it introduces a strategy for piece-wise linear scaling to allow other brains to be compared to the template brain that is featured in the atlas.

The Talairach-Tournoux coordinate system is comparable to, but [not exactly the same as the MNI coordinate system](http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach). It is defined using landmarks inside the brain and therefore can only be determined from an MRI scan, CT scan, or X-ray photo. This is in contrast to the external landmarks that are used for EEG/MEG recording. The landmarks used in the TT coordinate system are the anterior and posterior commisura (AC and PC) and the coordinate axes are defined according to

- the origin of the TT coordinate system is in the AC
Expand Down