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faq:how_are_the_different_head_and_mri_coordinate_systems_defined [2018/09/07 11:21]
robert [Summary]
faq:how_are_the_different_head_and_mri_coordinate_systems_defined [2018/09/07 11:27] (current)
robert re-ordered them alphabetically
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 See also [[http://​neuroimage.usc.edu/​brainstorm/​CoordinateSystems|this page]] from the BrainStorm documentation that also explains different MEG coordinate systems and [[http://​www.grahamwideman.com/​gw/​brain/​orientation/​orientterms.htm|this page]] that discusses orientations in MRI. See also [[http://​neuroimage.usc.edu/​brainstorm/​CoordinateSystems|this page]] from the BrainStorm documentation that also explains different MEG coordinate systems and [[http://​www.grahamwideman.com/​gw/​brain/​orientation/​orientterms.htm|this page]] that discusses orientations in MRI.
-==== Details of the CTF coordinate system ==== 
  
-The **CTF** coordinate system is expressed in centimeter (except the MRI which is in mm), with the principal (X, Y, Z) axes going through external landmarks (i.e. fiducials). ​These external landmarks ​are determined using the MEG measurement by placing small coils on them, and at the FCDC we usually place them on nasion and on a tube that extends from the left and right ear canal. Although the left and right ear markers do not really correspond to pre-auricular points (which is in front of the ear), they are referred to in the CTF software as LPA and RPA. The exact definition is+==== Details of the 4D/BTi coordinate system ==== 
 + 
 +The **4D Neuroimaging** (also known as BTi) coordinate system is expressed in meter, with the principal (X, Y, Z) axes going through external landmarks (i.e. fiducials). ​The details ​are
  
   * the origin is exactly between LPA and RPA   * the origin is exactly between LPA and RPA
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   * the Z-axis goes approximately towards the vertex, orthogonal to X and Y   * the Z-axis goes approximately towards the vertex, orthogonal to X and Y
  
-{{:faq:coordinatesystem_ctf.png?​200px|}} +{{:faq:coordinatesystem_bti.png?​200px|}}
-==== Details of the Neuromag coordinate system ====+
  
-The **Neuromag** ​coordinate system ​is expressed in meter, with the principal (X, Y, Z) axes going through external landmarks (i.e. fiducials). The details are+==== Details on the ACPC coordinate system ​====
  
-  * X-axis from the origin towards ​the RPA point (exactly through) +The ACPC coordinate system corresponds to that used in the Talairach atlas, but without ​the piecewise linear scaling applied to the brain, i.e. a brain in ACPC coordinates retains ​the individual shape and size. The landmarks used in the ACPC coordinate system are the anterior ​and posterior commisura (AC and PC) and the coordinate axes are defined according to
-  * Y-axis from the origin towards ​the nasion (exactly through) +
-  * Z-axis from the origin upwards orthogonal to the XY-plane +
-  * Origin: Intersection of the line through LPA and RPA and a line orthogonal to L passing through ​the nasion.+
  
-{{:​faq:​coordinatesystem_neuromag.png?​200px|}} +  * the origin ​of the TT coordinate system ​is in the AC 
-==== Details ​of the 4D/​BTi ​coordinate system ​====+  * the y-axis goes towards the front of the brain, along the line connecting PC and AC 
 +  * the z-axis goes towards the top of the brain 
 +  * the x-axis goes towards the right side of the brain 
 +  
 +See also this [[/​faq/​acpc|frequently asked question]].
  
-The **4D Neuroimaging** (also known as BTi) coordinate system ​is expressed in meter, with the principal (X, Y, Z) axes going through external landmarks (i.e. fiducials). The details are+ ==== Details on the Allen Institute mouse coordinate system ​====
  
-  * the origin ​is exactly between LPA and RPA +The Allen Institute has created a [[http://​scalablebrainatlas.incf.org/​ABA12|scalable mouse brain atlas (ABA12)]]. In this atlas, ​the coordinate system ​is defined as
-  * the X-axis goes towards NAS +
-  * 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+
  
-{{:​faq:​coordinatesystem_bti.png?​200px|}} +  * The origin ​of the coordinate system ​is at the [[http://​en.wikipedia.org/​wiki/​Bregma|Bregma point]]. 
-==== Details ​of the Yokogawa ​coordinate system ​====+  * The X-axis points from left (-) to right (+). 
 +  * The Y-axis points from posterior (-) to anterior (+). 
 +  * The Z-axis points from inferior (-) to superior (+).
  
-Unlike other systems, the **Yokogawa** system software does not automatically analyze its sensorlocations relative to fiducial coils. Instead the positions ​of the fiducial points are saved in an external textfile - in the helmet'​s own coordinate system ​- using the property menu of the YOKOGAWA MEG-VISION software. The details are+==== Details ​of the Analyze ​coordinate system ​====
  
-  ​the origin is at the center of the helmet +The **Analyze*coordinate system is defined by and used in the Analyze software developed by the [[http://​www.mayo.edu/​|Mayo Clinic]] (see also this [[http://​eeg.sourceforge.net/​ANALYZE75.pdf|pdf]]). The orientation is according to radiological conventions,​ and uses a left-handed coordinate system. The definition ​of the Analyze ​coordinate system ​is
-  ​the X-axis goes towards the nose +
-  ​* the Y-axis goes towards ​the left +
-  * the Z-axis goes towards the top of the head +
-==== Details of the Chieti ITAB coordinate system ​====+
  
-The **ITAB** coordinate system ​is expressed in meter, with the principal ​(X, Y, Zaxes going through external landmarks (i.efiducials)The details are+  ​the x-axis goes from right to left 
 +  ​the y-axis goes from posterior to anterior 
 +  ​the z-axis goes from inferior to superior 
 + 
 +Note that the Analyze ​*.img/*.hdr file format ​is also being used by other software ​(notably SPM), but the conventions of the coordinate systems may be differentTypically, fMRI specific software will use neurological conventions instead of radiological conventions.
  
-  * X-axis from the origin towards the RPA point (exactly through) 
-  * Y-axis from the origin towards the nasion (exactly through) 
-  * Z-axis from the origin upwards orthogonal to the XY-plane 
-  * Origin: Intersection of the line through LPA and RPA and a line orthogonal to L passing through the nasion. 
 ==== Details of the BESA coordinate system ==== ==== Details of the BESA coordinate system ====
  
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 See also [[http://​wiki.besa.de/​index.php?​title=Electrodes_and_Surface_Locations|this documentation]] on the BESA wiki.  See also [[http://​wiki.besa.de/​index.php?​title=Electrodes_and_Surface_Locations|this documentation]] on the BESA wiki. 
-==== Details of the Polhemus coordinate system ==== 
- 
-The **Polhemus** coordinate system as such does not exist. [[http://​www.polhemus.com|Polhemus]] is the company that manufactures electromagnetic 3-D trackers for a large variety of applications,​ and usually the trackers are sold to you by an EEG company. The EEG company bundles the tracker with specific software for recording the position of the electrodes. The software program communicates with the tracker, and presents the measured electrode locations on the computer screen and writes them to an ascii file. Therefore, the software determines the coordinate system that is used. It is common to require the user first to record external anatomical landmarks (i.e. fiducials) on the head: usually the left and right pre-auricular points and the nasion. Using there fiducials, the software can convert all subsequent electrode positions into a head coordinate system. 
- 
-The most common definition of the head coordinate system used by the software that accompanies the Polhemus tracker is 
- 
-  * the origin is exactly between LPA and RPA 
-  * the X-axis goes towards NAS 
-  * 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 CapTrack coordinate system ==== ==== Details of the CapTrack coordinate system ====
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 {{:​faq:​captrack.png?​nolink&​300|}} {{:​faq:​captrack.png?​nolink&​300|}}
  
 +==== Details of the Chieti ITAB coordinate system ====
 +
 +The **ITAB** coordinate system is expressed in meter, with the principal (X, Y, Z) axes going through external landmarks (i.e. fiducials). The details are
 +
 +  * X-axis from the origin towards the RPA point (exactly through)
 +  * Y-axis from the origin towards the nasion (exactly through)
 +  * Z-axis from the origin upwards orthogonal to the XY-plane
 +  * Origin: Intersection of the line through LPA and RPA and a line orthogonal to L passing through the nasion.
 +
 +==== Details of the CTF coordinate system ====
 +
 +The **CTF** coordinate system is expressed in centimeter (except the MRI which is in mm), with the principal (X, Y, Z) axes going through external landmarks (i.e. fiducials). These external landmarks are determined using the MEG measurement by placing small coils on them, and at the FCDC we usually place them on nasion and on a tube that extends from the left and right ear canal. Although the left and right ear markers do not really correspond to pre-auricular points (which is in front of the ear), they are referred to in the CTF software as LPA and RPA. The exact definition is
 +
 +  * the origin is exactly between LPA and RPA
 +  * the X-axis goes towards NAS
 +  * 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
 +
 +{{:​faq:​coordinatesystem_ctf.png?​200px|}}
  
 ==== Details of the DICOM coordinate system ==== ==== Details of the DICOM coordinate system ====
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   * z increases from inferior to superior   * z increases from inferior to superior
  
-==== Details of the Analyze ​coordinate system ====+==== Details of the FreeSurfer ​coordinate system ====
  
-The **Analyze** ​coordinate system is defined by and used in the Analyze software developed by the [[http://​www.mayo.edu/​|Mayo Clinic]] ​(see also this [[http://​eeg.sourceforge.net/​ANALYZE75.pdf|pdf]]). The orientation ​is according ​to radiological conventions,​ and uses left-handed coordinate systemThe definition ​of the Analyze ​coordinate system ​is+FreeSurfer is a software package that can be used to process anatomical MRIs, to obtain segmentations,​ cortical meshes, and inflated surfaces. ​The orientation of the coordinate system is RAS, and for volumetric ​(i.eanatomical MRIdata the origin ​is  ​defined ​to be the centre of 256x256x256 isotropic 1 mm volumeNote that if the head is not centered in the volume, the origin ​of the coordinate system ​will not coincide with the center of the head. 
  
-  * the x-axis goes from right to left +For surface based data FreeSurfer uses the tkrRAS coordinate system.
-  * the y-axis goes from posterior to anterior +
-  * the z-axis goes from inferior to superior+
  
-Note that the Analyze *.img/*.hdr file format ​is also being used by other software (notably SPM), but the conventions of the coordinate ​systems may be differentTypicallyfMRI specific ​software ​will use neurological conventions instead ​of radiological conventions.+See [[http://​www.grahamwideman.com/gw/​brain/​fs/​coords/​fscoords.htm|this page]] for more information about this. 
 + 
 +==== Details of the MNI coordinate system ==== 
 + 
 +The Montreal Neurological Institute coordinate system ​is comparable to, but not exactly ​the same as the Talairach-Tournoux ​coordinate ​systemRather than being based on a single specimenit is the result from spatially transforming and averaging MRI scans of many subjects. 
 + 
 +  * The origin of the MNI coordinate system is the anterior commissure 
 +  * The X-axis extends from the left side of the brain to the right side 
 +  * The Y-axis points from posterior to anterior 
 +  * The Z-axis points from inferior to superior 
 + 
 +See also this [[/​faq/​acpc|frequently asked question]]. 
 + 
 +Note that the SPM software ​makes use of the MNI coordinate system. 
 + 
 +==== Details of the Neuromag coordinate system ==== 
 + 
 +The **Neuromag** coordinate system is expressed in meter, with the principal (X, Y, Z) axes going through external landmarks (i.e. fiducials). The details are 
 + 
 +  * X-axis from the origin towards the RPA point (exactly through) 
 +  * Y-axis from the origin towards the nasion (exactly through) 
 +  * Z-axis from the origin upwards orthogonal to the XY-plane 
 +  * Origin: Intersection of the line through LPA and RPA and a line orthogonal to L passing through the nasion. 
 + 
 +{{:​faq:​coordinatesystem_neuromag.png?​200px|}}
  
 ==== Details of the NIfTI coordinate system ==== ==== Details of the NIfTI coordinate system ====
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 Note that this coordinate system applies when images are not registered to a standard space; if they are, the coordinate system of the relevant standard space applies (e.g. MNI or Talairach-Tournoux). See also [[https://​brainder.org/​2012/​09/​23/​the-nifti-file-format/​|here]] (search for "​Orientation information"​). Note that this coordinate system applies when images are not registered to a standard space; if they are, the coordinate system of the relevant standard space applies (e.g. MNI or Talairach-Tournoux). See also [[https://​brainder.org/​2012/​09/​23/​the-nifti-file-format/​|here]] (search for "​Orientation information"​).
-==== Details of the Talairach-Tournoux coordinate system ==== 
  
 +==== Details of the Polhemus coordinate system ====
 +
 +The **Polhemus** coordinate system as such does not exist. [[http://​www.polhemus.com|Polhemus]] is the company that manufactures electromagnetic 3-D trackers for a large variety of applications,​ and usually the trackers are sold to you by an EEG company. The EEG company bundles the tracker with specific software for recording the position of the electrodes. The software program communicates with the tracker, and presents the measured electrode locations on the computer screen and writes them to an ascii file. Therefore, the software determines the coordinate system that is used. It is common to require the user first to record external anatomical landmarks (i.e. fiducials) on the head: usually the left and right pre-auricular points and the nasion. Using there fiducials, the software can convert all subsequent electrode positions into a head coordinate system.
 +
 +The most common definition of the head coordinate system used by the software that accompanies the Polhemus tracker is
 +
 +  * the origin is exactly between LPA and RPA
 +  * the X-axis goes towards NAS
 +  * 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 Talairach-Tournoux coordinate system ====
  
 The [[https://​www.thieme.com/​books-main/​neurosurgery/​product/​414-co-planar-stereotaxic-atlas-of-the-human-brain|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 [[https://​www.thieme.com/​books-main/​neurosurgery/​product/​414-co-planar-stereotaxic-atlas-of-the-human-brain|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. ​
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 See also this [[/​faq/​acpc|frequently asked question]]. See also this [[/​faq/​acpc|frequently asked question]].
  
-==== Details of the MNI coordinate system ==== 
- 
-The Montreal Neurological Institute coordinate system is comparable to, but not exactly the same as the Talairach-Tournoux coordinate system. Rather than being based on a single specimen, it is the result from spatially transforming and averaging MRI scans of many subjects. 
- 
-  * The origin of the MNI coordinate system is the anterior commissure 
-  * The X-axis extends from the left side of the brain to the right side 
-  * The Y-axis points from posterior to anterior 
-  * The Z-axis points from inferior to superior 
- 
-See also this [[/​faq/​acpc|frequently asked question]]. 
- 
-Note that the SPM software makes use of the MNI coordinate system. 
-==== Details of the FreeSurfer coordinate system ==== 
- 
-FreeSurfer is a software package that can be used to process anatomical MRIs, to obtain segmentations,​ cortical meshes, and inflated surfaces. The orientation of the coordinate system is RAS, and for volumetric (i.e. anatomical MRI) data the origin is  defined to be the centre of a 256x256x256 isotropic 1 mm volume. Note that if the head is not centered in the volume, the origin of the coordinate system will not coincide with the center of the head.  
- 
-For surface based data FreeSurfer uses the tkrRAS coordinate system. 
- 
-See [[http://​www.grahamwideman.com/​gw/​brain/​fs/​coords/​fscoords.htm|this page]] for more information about this. 
 ==== Details on the Paxinos-Franklin mouse coordinate system ==== ==== Details on the Paxinos-Franklin mouse coordinate system ====
  
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      ];      ];
  
 +==== Details of the Yokogawa coordinate system ====
  
-  +Unlike other systems, ​the **Yokogawa** system software does not automatically analyze its sensorlocations relative to fiducial coils. Instead the positions of the fiducial points are saved in an external textfile - in the helmet'​s own coordinate system ​- using the property menu of the YOKOGAWA MEG-VISION software. The details are
-==== Details on the Allen Institute mouse coordinate system ​====+
  
-The Allen Institute has created a [[http://​scalablebrainatlas.incf.org/​ABA12|scalable mouse brain atlas (ABA12)]]. In this atlas, ​the coordinate system is defined as +  * the origin is at the center ​of the helmet 
- +  * the X-axis goes towards the nose 
-  * The origin ​of the coordinate system ​is at the [[http://​en.wikipedia.org/​wiki/​Bregma|Bregma point]]. +  * the Y-axis goes towards the left 
-  * The X-axis points from left (-) to right (+). +  * the Z-axis goes towards the top of the head
-  * The Y-axis points from posterior (-) to anterior (+). +
-  * The Z-axis points from inferior (-) to superior (+). +
- +
-==== Details on the ACPC coordinate system ==== +
- +
-The ACPC coordinate system corresponds to that used in the Talairach atlas, but without the piecewise linear scaling applied to the brain, i.e. a brain in ACPC coordinates retains the individual shape and size. The landmarks used in the ACPC 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 +
-  * the y-axis goes towards the front of the brain, along the line connecting PC and AC +
-  * the z-axis goes towards the top of the brain +
-  * the x-axis goes towards the right side of the brain +
-  +
-See also this [[/​faq/​acpc|frequently asked question]].+