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| == Glossary == | <<<TableOfContents>>> |
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| '''anatomically derived defect:''' A topological defect in the cortical surface that arises from a feature of normal neuroanatomy to be distinguished from defects arising entirely from segmentation errors. See '''topological defect'''. |
== anatomically derived defect == A topological defect in the cortical surface that arises from a feature of normal neuroanatomy to be distinguished from defects arising entirely from segmentation errors. See topological defect |
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| '''artifact:''' A feature that appears in an image but is not actually present in the imaged object. |
== artifact == A feature that appears in an image but is not actually present in the imaged object. |
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| '''average convexity:''' The signed distance that a vertex moves during the inflation process. |
== average convexity == The signed distance that a vertex moves during the inflation process. |
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| '''brain volume:''' The T1 volume after the skull and other non-brain structures have been removed. This volume can be viewed using tkmedit. |
== brain volume == The T1 volume after the skull and other non-brain structures have been removed. This volume can be viewed using tkmedit. |
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| '''canonical surface:''' Surface-based atlas constructed from the cortical surfaces of 40 normal individuals (used for inter-subject averaging). |
== canonical surface == Surface-based atlas constructed from the cortical surfaces of 40 normal individuals (used for inter-subject averaging). |
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| '''conversion/averaging:''' Process of converting and averaging multiple structural acquisitions from the native magnet format into the native FreeSurfer format (see COR files). |
== conversion/averaging == Process of converting and averaging multiple structural acquisitions from the native magnet format into the native FreeSurfer format (see COR files). |
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| '''COR files:''' The native file format used by FreeSurfer to store 3D structural image data. |
== COR files == The native file format used by FreeSurfer to store 3D structural image data. |
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| '''Euler number:''' After Leonhard Euler (1707-83). A topological invariant of a surface that can be computed from the number of edges, vertices and faces in a polygonal tessellation (command mris_euler_number). The Euler number of a sphere will equal 2; the Euler number of a surface with n handles is 2 2n. |
== Euler number == After Leonhard Euler (1707-83). A topological invariant of a surface that can be computed from the number of edges, vertices and faces in a polygonal tessellation (command [[http://surfer.nmr.mgh.harvard.edu/fswiki/mris_euler_number|mris_euler_number]] ). The Euler number of a sphere will equal 2; the Euler number of a surface with n handles is 2 2n. |
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| '''filled volume:''' The wm volume after separation of the left and right hemispheres and filling of each hemisphere. This volume can be viewed using tkmedit. |
== filled volume == The wm volume after separation of the left and right hemispheres and filling of each hemisphere. This volume can be viewed using tkmedit. |
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| '''flattening:''' Producing a planar (flat) representation of a patch of the cortical surface that has minimal metric distortion. |
== flattening == Producing a planar (flat) representation of a patch of the cortical surface that has minimal metric distortion. |
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| '''gyrus:''' A fold or convolution of brain tissue (an outward folded region). |
== gyrus == A fold or convolution of brain tissue (an outward folded region). |
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| '''inflated surface:''' The smoothwm surface after inflation. This surface can be viewed using surfer. |
== inflated surface == The smoothwm surface after inflation. This surface can be viewed using surfer. |
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| '''inflation:''' The process of smoothing the cortex while minimizing metric distortion, so that all sulci are fully visible and surface distances are apparent to visual inspection. |
== inflation == The process of smoothing the cortex while minimizing metric distortion, so that all sulci are fully visible and surface distances are apparent to visual inspection. |
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| '''intensity:''' Measured amount of magnetic field at a given spatial location, represented by a voxel (higher SNRsignal to noise ratio means voxels will have a higher intensity relative to the background noise, and appear brighter). |
== intensity == Measured amount of magnetic field at a given spatial location, represented by a voxel (higher SNR signal to noise ratio means voxels will have a higher intensity relative to the background noise, and appear brighter). |
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| '''label:''' A particular region of interest. e.g. in tksurfer the label would be a region of interest in the surface. In tkmedit a label is a region of interest in the volume. |
== label == A particular region of interest. e.g. in tksurfer the label would be a region of interest in the surface. In tkmedit a label is a region of interest in the volume. |
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| '''morphing:''' Computer graphics technique whereby a mapping is computed that smoothly transforms one image or surface into another. |
== morphing == Computer graphics technique whereby a mapping is computed that smoothly transforms one image or surface into another. |
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| '''morphometrics:''' The study of geometric properties of the human brain. |
== morphometrics == The study of geometric properties of the human brain. |
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| '''motion correction:''' Processing multiple structural volumes so that the effects of subject movement are minimized. This is typically done by aligning multiple images/volume to an initial image/volume (see conversion/averaging). |
== motion correction == Processing multiple structural volumes so that the effects of subject movement are minimized. This is typically done by aligning multiple images/volume to an initial image/volume (see conversion/averaging). |
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| '''MRI volume:''' The three dimensional volumetric data set collected from a MRI scanner. |
== MRI volume == The three dimensional volumetric data set collected from a MRI scanner. |
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| '''orig volume:''' The original MRI volume. This volume can be viewed using tkmedit. |
== orig volume == The original MRI volume. This volume can be viewed using tkmedit. |
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| '''orig surface:''' The first surface constructed by covering the labeled voxels in the filled volume. This surface can be viewed using surfer. |
== orig surface == The first surface constructed by covering the labeled voxels in the filled volume. This surface can be viewed using surfer. |
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| '''pial:''' Pertaining to the delicate pia mater which envelops the brain (gray matter). Also, the model of the pial surface (?h.pial). |
== pial == Pertaining to the delicate pia mater which envelops the brain (gray matter). Also, the model of the pial surface (?h.pial). |
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| '''pial surface:''' The refined estimate of the gray/CSF boundary (pial surface). This surface can be viewed using surfer. |
== pial surface == The refined estimate of the gray/CSF boundary (pial surface). This surface can be viewed using surfer. |
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| '''region growing process:''' An algorithm that groups voxels or sub-regions into larger regions. |
== region growing process == An algorithm that groups voxels or sub-regions into larger regions. |
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| '''RF-field inhomogeneities:''' Spatial variations in the Radio Frequency (RF) excitation pulse. These variations result in changes in the measured intensity for a given tissue class that are related to the spatial location of the voxel. |
== RF-field inhomogeneities == Spatial variations in the Radio Frequency (RF) excitation pulse. These variations result in changes in the measured intensity for a given tissue class that are related to the spatial location of the voxel. |
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| '''segmentation:''' Labeling of tissue classes from MRI data (e.g. white matter). |
== segmentation == Labeling of tissue classes from MRI data (e.g. white matter). |
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| '''smoothing:''' Process of producing a relatively even and regular cortical surface. |
== smoothing == Process of producing a relatively even and regular cortical surface. |
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| '''smoothwm surface:''' The orig surface after smoothing. This surface can be viewed using surfer. |
== smoothwm surface == The orig surface after smoothing. This surface can be viewed using surfer. |
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| '''sulcus:''' A groove or furrow in brain tissue (an inward folded region). |
== sulcus == A groove or furrow in brain tissue (an inward folded region). |
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| '''supertessellated icosahedron:''' Polygonal approximation to a sphere. |
== supertessellated icosahedron == Polygonal approximation to a sphere. |
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| '''T1:''' Longitudinal relaxation constant. |
== T1 == Longitudinal relaxation constant. |
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| '''T1 volume:''' The MRI volume after intensity normalization. This volume can be viewed using tkmedit. |
== T1 volume == The MRI volume after intensity normalization. This volume can be viewed using tkmedit. |
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| '''T1 Weighted Image:''' A magnetic resonance image where the contrast is predominantly dependent on T1. |
== T1 Weighted Image == A magnetic resonance image where the contrast is predominantly dependent on T1. |
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| '''T2 Weighted Image:''' A magnetic resonance image where the contrast is predominantly dependent on T2. |
== T2 Weighted Image == A magnetic resonance image where the contrast is predominantly dependent on T2. |
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| '''T2:''' Transverse relaxation constant. |
== T2 == Transverse relaxation constant. |
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| '''Talairach coordinate:''' The corresponding location in the Talairach atlas for a given point in a brain that has been coregistered with the atlas (Talairach et al, 1967). |
== Talairach coordinate == The corresponding location in the Talairach atlas for a given point in a brain that has been coregistered with the atlas (Talairach et al, 1967). |
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| '''tessellation:''' Covering of a surface by repeated use of a single shape. |
== tessellation == Covering of a surface by repeated use of a single shape. |
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| '''topology:''' The properties of a surface related to its connectivity that are unaffected by geometric (i.e. rubber sheet) transformations. |
== topology == The properties of a surface related to its connectivity that are unaffected by geometric (i.e. rubber sheet) transformations. |
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| '''topological defect:''' A portion of a surface that results in the surface topology differing from that of a sphere. |
== topological defect == A portion of a surface that results in the surface topology differing from that of a sphere. |
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| '''volume:''' A 3-D data set that typically contains either intensity information derived from the original MRI, or the results of segmenting this data into tissue classes. |
== volume == A 3-D data set that typically contains either intensity information derived from the original MRI, or the results of segmenting this data into tissue classes. |
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| '''voxel:''' The basic element of an MRI volume (analogous to a pixel in a 2-D image). The volume of a structural voxel is approximately 1 mm^3^. |
== voxel == The basic element of an MRI volume (analogous to a pixel in a 2-D image). The volume of a structural voxel is approximately 1 mm^3^. |
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| '''white surface:''' The refined estimate of the gray/white boundary. This surface can be viewed using surfer. |
== white surface == The refined estimate of the gray/white boundary. This surface can be viewed using surfer. |
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|
'''wm volume:''' The brain volume after white matter segmentation. This is also the volume that is manually edited. This volume can be viewed using tkmedit. |
== wm volume == The brain volume after white matter segmentation. This is also the volume that is manually edited. This volume can be viewed using tkmedit. |
<
Contents
- anatomically derived defect
- artifact
- average convexity
- brain volume
- canonical surface
- conversion/averaging
- COR files
- Euler number
- filled volume
- flattening
- gyrus
- inflated surface
- inflation
- intensity
- label
- morphing
- morphometrics
- motion correction
- MRI volume
- orig volume
- orig surface
- pial
- pial surface
- region growing process
- RF-field inhomogeneities
- segmentation
- smoothing
- smoothwm surface
- sulcus
- supertessellated icosahedron
- T1
- T1 volume
- T1 Weighted Image
- T2 Weighted Image
- T2
- Talairach coordinate
- tessellation
- topology
- topological defect
- volume
- voxel
- white surface
- wm volume
>
anatomically derived defect
- A topological defect in the cortical surface that arises from a feature of normal neuroanatomy to be distinguished from defects arising entirely from segmentation errors. See topological defect
artifact
- A feature that appears in an image but is not actually present in the imaged object.
average convexity
- The signed distance that a vertex moves during the inflation process.
brain volume
- The T1 volume after the skull and other non-brain structures have been removed. This volume can be viewed using tkmedit.
canonical surface
- Surface-based atlas constructed from the cortical surfaces of 40 normal individuals (used for inter-subject averaging).
conversion/averaging
Process of converting and averaging multiple structural acquisitions from the native magnet format into the native FreeSurfer format (see COR files).
COR files
The native file format used by FreeSurfer to store 3D structural image data.
Euler number
After Leonhard Euler (1707-83). A topological invariant of a surface that can be computed from the number of edges, vertices and faces in a polygonal tessellation (command mris_euler_number ). The Euler number of a sphere will equal 2; the Euler number of a surface with n handles is 2 2n.
filled volume
- The wm volume after separation of the left and right hemispheres and filling of each hemisphere. This volume can be viewed using tkmedit.
flattening
- Producing a planar (flat) representation of a patch of the cortical surface that has minimal metric distortion.
gyrus
- A fold or convolution of brain tissue (an outward folded region).
inflated surface
- The smoothwm surface after inflation. This surface can be viewed using surfer.
inflation
- The process of smoothing the cortex while minimizing metric distortion, so that all sulci are fully visible and surface distances are apparent to visual inspection.
intensity
- Measured amount of magnetic field at a given spatial location, represented by a voxel (higher SNR signal to noise ratio means voxels will have a higher intensity relative to the background noise, and appear brighter).
label
- A particular region of interest. e.g. in tksurfer the label would be a region of interest in the surface. In tkmedit a label is a region of interest in the volume.
morphing
- Computer graphics technique whereby a mapping is computed that smoothly transforms one image or surface into another.
morphometrics
- The study of geometric properties of the human brain.
motion correction
- Processing multiple structural volumes so that the effects of subject movement are minimized. This is typically done by aligning multiple images/volume to an initial image/volume (see conversion/averaging).
MRI volume
- The three dimensional volumetric data set collected from a MRI scanner.
orig volume
- The original MRI volume. This volume can be viewed using tkmedit.
orig surface
- The first surface constructed by covering the labeled voxels in the filled volume. This surface can be viewed using surfer.
pial
- Pertaining to the delicate pia mater which envelops the brain (gray matter). Also, the model of the pial surface (?h.pial).
pial surface
- The refined estimate of the gray/CSF boundary (pial surface). This surface can be viewed using surfer.
region growing process
- An algorithm that groups voxels or sub-regions into larger regions.
RF-field inhomogeneities
- Spatial variations in the Radio Frequency (RF) excitation pulse. These variations result in changes in the measured intensity for a given tissue class that are related to the spatial location of the voxel.
segmentation
- Labeling of tissue classes from MRI data (e.g. white matter).
smoothing
- Process of producing a relatively even and regular cortical surface.
smoothwm surface
- The orig surface after smoothing. This surface can be viewed using surfer.
sulcus
- A groove or furrow in brain tissue (an inward folded region).
supertessellated icosahedron
- Polygonal approximation to a sphere.
T1
- Longitudinal relaxation constant.
T1 volume
- The MRI volume after intensity normalization. This volume can be viewed using tkmedit.
T1 Weighted Image
- A magnetic resonance image where the contrast is predominantly dependent on T1.
T2 Weighted Image
- A magnetic resonance image where the contrast is predominantly dependent on T2.
T2
- Transverse relaxation constant.
Talairach coordinate
- The corresponding location in the Talairach atlas for a given point in a brain that has been coregistered with the atlas (Talairach et al, 1967).
tessellation
- Covering of a surface by repeated use of a single shape.
topology
- The properties of a surface related to its connectivity that are unaffected by geometric (i.e. rubber sheet) transformations.
topological defect
- A portion of a surface that results in the surface topology differing from that of a sphere.
volume
- A 3-D data set that typically contains either intensity information derived from the original MRI, or the results of segmenting this data into tissue classes.
voxel
The basic element of an MRI volume (analogous to a pixel in a 2-D image). The volume of a structural voxel is approximately 1 mm3.
white surface
- The refined estimate of the gray/white boundary. This surface can be viewed using surfer.
wm volume
- The brain volume after white matter segmentation. This is also the volume that is manually edited. This volume can be viewed using tkmedit.