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| * Labels: * Color Lookup Tables * Annotation Files |
== Label == A label is an integer value which can be associated with a surface mesh vertex, or with a voxel, to indicate that it belongs to some region of interest. This could mark the vertex or voxel as part of an anatomical region, or it could mark the vertex/voxel as part of a region for analysis. Sometimes when speaking or writing loosely, the word "label" is used as shorthand for "the set of vertices marked with a particular label". Sometimes vertices are said to "belong to a label", meaning that these vertics belong to the set marked by that label. "Saving a label" refers to saving into a file the list of vertices marked by a particular label value. == Label file == A label file is a text file capturing a list of vertices belonging to a region, including their spatial positions(using R,A,S coordinates). Because both vertex number and corresponding position are listed, a label file can be used by either tksurfer or tkmedit to identify surface or volume locations belonging to the region. It should be noted that a label file's vertex numbers will apply to several surfaces of a subject: for example the white surface, the pial surface, the inflated surface and so on. However the R,A,S positions are those of a particular one of these surfaces, according to selections in effect when the label file was saved by tksurfer. Perhaps surprisingly, a label file contains neither the label code nor label name that it pertains to. Instead it is conventional to name the label file in a manner that indicates the label intended, though this naming convention has varied over the years. Examples: * lh.cortex.label * lh-avg_calcarine_sulcus.label. === Label file format === {{{ #!ascii label , from subject 1806 7 -22.796 -66.405 -29.582 0.000000 89 -22.273 -43.118 -24.069 0.000000 138 -14.142 -81.495 -30.903 0.000000 [...] }}} ||'''Row'''||'''Col1'''||'''Col2'''||'''Col3'''||'''Col4'''||'''Col5'''|| ||1||Comment|| || || || || ||2||Count of subsequent rows|| || || || || ||3..end||Vertex num||R coord||A coord||S coord||Don't know|| == Color Lookup Table == In FreeSurfer a "color lookup table" is a table cross-referencing the integer label code to a name, and to a color (Red, Green, Blue and Opacity values). Although called a "color lookup", in many usages it is the cross-reference to name, or simply the list of names, which is important. * Annotation: An annotation |
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| == Annotations == | x == Annotations == x |
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| * EditingLabels : Pointers to a couple of pages about labels | * EditingLabels : Pointers to a couple of pages about labels |
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| = Synopsis = command argA argB -flag1 arg1 -flag2 arg2 [-flag3 arg3] [-flag4 arg4] |
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| = Arguments = == Positional Arguments == || argA || brief description || detailed description (eg, help file information) || || argB || brief description || detailed description (eg, help file information) || == Required Flagged Arguments == || -flag1 arg1 || brief description || detailed description (eg, help file information) || || -flag2 arg2 || brief description || detailed description (eg, help file information) || == Optional Flagged Arguments == || -flag3 arg3 || brief description ||detailed description (eg, help file information) || || -flag4 arg4 || brief description ||detailed description (eg, help file information) || = Outputs = || volume1 || description || || volume2 || description || = Description = description = Examples = == Example 1 == command foo -i f -o out description == Example 2 == command foo -i f -o out -f fvalue description = Bugs = None = See Also = ["othercommand1"], ["othercommand2"] = Links = FreeSurfer, FsFast = Methods Description = {{{ description description }}} = References = ["References/Lastname###"] = Reporting Bugs = Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> = Author/s = JaneSmith |
= Document Author/s = GrahamWideman |
Index TableOfContents
Labels, Color Lookup Tables and Annotation Files
This page discusses the basic concepts of FreeSurfer files that relate to identifying regions-of-interest for surfaces and volumes.
Label
A label is an integer value which can be associated with a surface mesh vertex, or with a voxel, to indicate that it belongs to some region of interest. This could mark the vertex or voxel as part of an anatomical region, or it could mark the vertex/voxel as part of a region for analysis.
Sometimes when speaking or writing loosely, the word "label" is used as shorthand for "the set of vertices marked with a particular label". Sometimes vertices are said to "belong to a label", meaning that these vertics belong to the set marked by that label. "Saving a label" refers to saving into a file the list of vertices marked by a particular label value.
Label file
A label file is a text file capturing a list of vertices belonging to a region, including their spatial positions(using R,A,S coordinates). Because both vertex number and corresponding position are listed, a label file can be used by either tksurfer or tkmedit to identify surface or volume locations belonging to the region.
It should be noted that a label file's vertex numbers will apply to several surfaces of a subject: for example the white surface, the pial surface, the inflated surface and so on. However the R,A,S positions are those of a particular one of these surfaces, according to selections in effect when the label file was saved by tksurfer.
Perhaps surprisingly, a label file contains neither the label code nor label name that it pertains to. Instead it is conventional to name the label file in a manner that indicates the label intended, though this naming convention has varied over the years. Examples:
- lh.cortex.label
- lh-avg_calcarine_sulcus.label.
Label file format
1806 7 -22.796 -66.405 -29.582 0.000000 89 -22.273 -43.118 -24.069 0.000000 138 -14.142 -81.495 -30.903 0.000000 [...]
Row |
Col1 |
Col2 |
Col3 |
Col4 |
Col5 |
1 |
Comment |
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|
2 |
Count of subsequent rows |
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|
|
|
3..end |
Vertex num |
R coord |
A coord |
S coord |
Don't know |
Color Lookup Table
In FreeSurfer a "color lookup table" is a table cross-referencing the integer label code to a name, and to a color (Red, Green, Blue and Opacity values). Although called a "color lookup", in many usages it is the cross-reference to name, or simply the list of names, which is important.
- Annotation: An annotation
Details
Labels
x
Color Lookup Tables
x
Annotations
x
Related pages
AnnotFiles : Some brief end-user notes on annotation files, plus MatLab and C developer notes.
- ["mris_label2annot"] : Documentation for the command-line program that amalgamates label files (plus optional color lookup table file) into a single annotation file.
- ["mri_annotation2label"] : Documentation for the command-line program that breaks an annotation file into individual label files
EditingLabels : Pointers to a couple of pages about labels
TkSurferGuide/TkSurferWorkingWithData/TkSurferLabel : Working with labels