|
Size: 438
Comment: new page for cortical parcellation
|
Size: 1783
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
| 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 |
| Line 7: | Line 11: |
| <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. |
| Line 9: | Line 13: |
| <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. |
| Line 11: | Line 15: |
| == Binaries == | == Utilities == |
| Line 13: | Line 17: |
| [wiki:Self:mris_ca_train mris_ca_train] | * ["mris_sample_parc"] - samples a volumetric parcellation onto a surface |
| Line 15: | Line 19: |
| [wiki:Self:mris_ca_label mris_ca_label] | * ["mris_ca_train"] - creates the reference atlas |
| Line 17: | Line 21: |
| == Atlas == | * ["mris_ca_label"] - parcellates a cortical surface based on the reference atlas |
| Line 19: | Line 23: |
| discuss default atlas, discuss creation of own atlas | == Atlases == |
| Line 21: | Line 25: |
| == FAQ == * What if I have a labeled volume? |
* 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"]. |
[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"].