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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 (produces .gcs files) |
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| == Atlas == | * ["mris_ca_label"] - parcellates a cortical surface based on the reference atlas (produces .annot files) |
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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 (created in-house using mris_ca_train): * $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"]. See also: SurfaceRegAndTemplates |
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| * What if I have a labeled volume? | == .annot files == After Freesurfer processes a subject, in the subject's /label directory, there are .annot files containing the parcellation data for each hemishere. The ?h.aparc.annot files contain the desikan_killiany.gcs parcellation scheme, while the ?h.aparc.a2005s.annot files contain the atlas2005_simple.gcs scheme. The data in the .annot files can be read using the matlab script attachment:read_annotation.m (also found in $FREESURFER_HOME/matlab). Example usage: {{{ >> [vertices,label,colortable]=read_annotation('rh.aparc.annot'); }}} Where {{{vertices}}} is just each vertex number. {{{label}}} contains the parcellation label for that vertex, where the label is a {{{colortable}}} number. For instance, if a label is '6553700', then find that number in the {{{colortable.table}}} structure, and its label name is that same index in the {{{colortable.struct_name}}} structure (in this example, '6553700' is 'frontalpole'). == 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 (produces .gcs files)
- ["mris_ca_label"] - parcellates a cortical surface based on the reference atlas (produces .annot files)
Atlases
- There are two atlases included with Freesurfer (created in-house using mris_ca_train):
$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"]. See also: SurfaceRegAndTemplates
.annot files
After Freesurfer processes a subject, in the subject's /label directory, there are .annot files containing the parcellation data for each hemishere. The ?h.aparc.annot files contain the desikan_killiany.gcs parcellation scheme, while the ?h.aparc.a2005s.annot files contain the atlas2005_simple.gcs scheme. The data in the .annot files can be read using the matlab script attachment:read_annotation.m (also found in $FREESURFER_HOME/matlab). Example usage:
>> [vertices,label,colortable]=read_annotation('rh.aparc.annot');Where vertices is just each vertex number. label contains the parcellation label for that vertex, where the label is a colortable number. For instance, if a label is '6553700', then find that number in the colortable.table structure, and its label name is that same index in the colortable.struct_name structure (in this example, '6553700' is 'frontalpole').
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)