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| Automated parcellation of cerebral cortex into specific neuroanatomical regions of interest. | = Cortical Parcellation = The FreeSurfer utilities ["mris_ca_train"] and ["mris_ca_label"] together implement a technique for automatically assigning a neuroanatomical label to each location on a cortical surface model based on probabilistic information estimated from a manually labeled training set (made using FreeSurfer). This procedure incorporates both geometric information derived from the cortical model, and neuroanatomical convention, as found in the training set. The result is a complete labeling of cortical sulci and gyri. attachment:annot-sm.jpg |
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| <add link to fischl paper> | * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Automatically Parcellating the Human Cerebral Cortex], Fischl et al., (2004). Cerebral Cortex, 14:11-22. |
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| <add link to desikan paper> | * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest], Desikan et al., (2006). NeuroImage, in press. |
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| == Binaries == | == Utilities == |
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| [wiki:Self:mris_ca_train mris_ca_train] | * ["mris_sample_parc"] - samples a volumetric parcellation onto a surface |
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| [wiki:Self:mris_ca_label mris_ca_label] | * ["mris_ca_train"] - creates the reference atlas |
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| == Atlas == | * ["mris_ca_label"] - parcellates a cortical surface based on the reference atlas |
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| discuss default atlas, discuss creation of own atlas | == Atlases == |
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| == FAQ == | * There are two atlases included with Freesurfer: * $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs - see [https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf Desikan et al., (2006)]. * $FREESURFER_HOME/average/?h.atlas2005_simple.gcs - see [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Fischl et al., (2004)]. * To create your own atlas, see the example in ["mris_ca_train"]. |
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| * What if I have a labeled volume? | == Lobe mapping == While some ROIs cross two or more lobar boundaries (i.e. fusiform), others (i.e. cingulate subdivisions) can be considered separately or can be included to follow the 4 lobes. The following is an approximate mapping of individual ROIs (found in ?h.aparc.annot) to the lobes: === Frontal === * Superior Frontal * Rostral and Caudal Middle Frontal * Pars Opercularis, Pars Triangularis, and Pars Orbitalis * Lateral and Medial Orbitofrontal * Precentral * Paracentral * Frontal Pole === Parietal === * Superior Parietal * Inferior Parietal * Supramarginal * Postcentral * Precuneus === Temporal === * Superior, Middle, and Inferior Temporal * Fusiform * Transverse Temporal * Entorhinal * Temporal Pole * Parahippocampal === Occipital === * Lateral Occipital * Lingual * Cuneus * Pericalcarine === Cingulate (if you want to include in a lobe) === * Rostral Anterior (Frontal) * Caudal Anterior (Frontal) * Posterior (Parietal) * Isthmus (Parietal) |
[wiki:FreeSurferWiki top]
Cortical Parcellation
The FreeSurfer utilities ["mris_ca_train"] and ["mris_ca_label"] together implement a technique for automatically assigning a neuroanatomical label to each location on a cortical surface model based on probabilistic information estimated from a manually labeled training set (made using FreeSurfer). This procedure incorporates both geometric information derived from the cortical model, and neuroanatomical convention, as found in the training set. The result is a complete labeling of cortical sulci and gyri.
attachment:annot-sm.jpg
Background
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Automatically Parcellating the Human Cerebral Cortex], Fischl et al., (2004). Cerebral Cortex, 14:11-22.
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest], Desikan et al., (2006). NeuroImage, in press.
Utilities
- ["mris_sample_parc"] - samples a volumetric parcellation onto a surface
- ["mris_ca_train"] - creates the reference atlas
- ["mris_ca_label"] - parcellates a cortical surface based on the reference atlas
Atlases
- There are two atlases included with Freesurfer:
$FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs - see [https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf Desikan et al., (2006)].
$FREESURFER_HOME/average/?h.atlas2005_simple.gcs - see [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Fischl et al., (2004)].
- To create your own atlas, see the example in ["mris_ca_train"].
Lobe mapping
While some ROIs cross two or more lobar boundaries (i.e. fusiform), others (i.e. cingulate subdivisions) can be considered separately or can be included to follow the 4 lobes. The following is an approximate mapping of individual ROIs (found in ?h.aparc.annot) to the lobes:
Frontal
- Superior Frontal
- Rostral and Caudal Middle Frontal
- Pars Opercularis, Pars Triangularis, and Pars Orbitalis
- Lateral and Medial Orbitofrontal
- Precentral
- Paracentral
- Frontal Pole
Parietal
- Superior Parietal
- Inferior Parietal
- Supramarginal
- Postcentral
- Precuneus
Temporal
- Superior, Middle, and Inferior Temporal
- Fusiform
- Transverse Temporal
- Entorhinal
- Temporal Pole
- Parahippocampal
Occipital
- Lateral Occipital
- Lingual
- Cuneus
- Pericalcarine
Cingulate (if you want to include in a lobe)
- Rostral Anterior (Frontal)
- Caudal Anterior (Frontal)
- Posterior (Parietal)
- Isthmus (Parietal)