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| = Name = command - 1/2 sentence summary |
= mris_label2annot= This command-line program consolidates one or more label files, plus optionally a color lookup table, into a single annotation file. |
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| || argA || brief description || detailed description (eg, help file information) || || argB || brief description || detailed description (eg, help file information) || |
none |
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| == Required Flagged Arguments == || -flag1 arg1 || brief description || detailed description (eg, help file information) || || -flag2 arg2 || brief description || detailed description (eg, help file information) || |
== Flagged Arguments == ||<^>'''Category'''||<^>'''Flag'''||<^> <'''Args'''> ||<^>'''Description'''|| ||<^>Input||<^>--ctab||<^> <ctab_file> ||<^>Colortable file. File that defines the structure names, their indices, and their color. This must have the same format as that found in $FREESUFER_HOME/FreeSurferColorLUT.txt. [[BR]]The colortable file gets incorporated into the output annotation file. In addition, depending on other options, the names in colortable can be used by this program to find correspondingly-named label files. More details below.|| ||<^>Input||<^>--l||<^> <label_file> ||<^>Repeat this flag and arg for each additional label file you want to include in the annotation file.|| ||<^>Input||<^>--ldir||<^> <labeldir> ||<^>When seeking label files based on names in ctab, find the label files in labeldir. This has no effect on the files specified by --l|| ||<^>Input||<^>--ldir-default||<^> ||<^>Works like --ldir option, setting labeldir to the default label directory for the selected subject:[[BR]][[BR]]{SUBJECTS_DIR}/{SUBJECT}/label|| ||<^>Input||<^>--s or --subject||<^> <subject> ||<^>FreeSurfer subject to work on|| ||<^>Output||<^>--a or --annot||<^> <annot_name> ||<^>output annotation file The actual file will be called 'hemi.annot_name.annot', and it will be created in directory subject/label. To avoid overwriting possibly valuable data, the program will not overwrite an existing file by the same name.|| ||<^>Output||<^>--h or --hemi||<^> <hemi> ||<^>hemisphere (lh or rh)|| ||<^>Algorithm||<^>--no-unknown||<^> ||<^>Start label numbering at index 0 instead of index 1. Do not map unhit vertices (ie, vertices without a label) to 0.|| ||<^>Utility||<^>--help||<^> ||<^>print_help|| ||<^>Utility||<^>--version||<^> ||<^>print_version|| ||<^>Advanced||<^>--checkopts||<^> ||<^>checkoptsonly = 1|| ||<^>Advanced||<^>--debug||<^> ||<^>debug = 1|| ||<^>Advanced||<^>--nhits||<^> <NHitsFile> ||<^>This option creates a diagnostic file showing whether the cumulative effect of all the label files happens to assign more than one label to each vertex. The output file is a FreeSurfer 'overlay' format file, in which each vertex has an associated value, in this case the count of labels assigned to that vertex. This can be displayed in tksurfer as a color. Setting fthresh to 1.5 will distinguish good vertices (count<=1) from bad (count>=2).|| ||<^>Advanced||<^>--nocheckopts||<^> ||<^>checkoptsonly = 0|| ||<^>||<^>XXXXXXXXXXXXX||<^> ||<^>|| |
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| == Optional Flagged Arguments == || -flag3 arg3 || brief description ||detailed description (eg, help file information) || || -flag4 arg4 || brief description ||detailed description (eg, help file information) || |
Index TableOfContents
= mris_label2annot= This command-line program consolidates one or more label files, plus optionally a color lookup table, into a single annotation file.
Synopsis
command argA argB -flag1 arg1 -flag2 arg2 [-flag3 arg3] [-flag4 arg4]
Arguments
Positional Arguments
none
Flagged Arguments
Category |
Flag |
<Args> |
Description |
Input |
--ctab |
<ctab_file> |
Colortable file. File that defines the structure names, their indices, and their color. This must have the same format as that found in $FREESUFER_HOME/FreeSurferColorLUT.txt. BRThe colortable file gets incorporated into the output annotation file. In addition, depending on other options, the names in colortable can be used by this program to find correspondingly-named label files. More details below. |
Input |
--l |
<label_file> |
Repeat this flag and arg for each additional label file you want to include in the annotation file. |
Input |
--ldir |
<labeldir> |
When seeking label files based on names in ctab, find the label files in labeldir. This has no effect on the files specified by --l |
Input |
--ldir-default |
|
Works like --ldir option, setting labeldir to the default label directory for the selected subject:BRBR{SUBJECTS_DIR}/{SUBJECT}/label |
Input |
--s or --subject |
<subject> |
FreeSurfer subject to work on |
Output |
--a or --annot |
<annot_name> |
output annotation file The actual file will be called 'hemi.annot_name.annot', and it will be created in directory subject/label. To avoid overwriting possibly valuable data, the program will not overwrite an existing file by the same name. |
Output |
--h or --hemi |
<hemi> |
hemisphere (lh or rh) |
Algorithm |
--no-unknown |
|
Start label numbering at index 0 instead of index 1. Do not map unhit vertices (ie, vertices without a label) to 0. |
Utility |
--help |
|
print_help |
Utility |
--version |
|
print_version |
Advanced |
--checkopts |
|
checkoptsonly = 1 |
Advanced |
--debug |
|
debug = 1 |
Advanced |
--nhits |
<NHitsFile> |
This option creates a diagnostic file showing whether the cumulative effect of all the label files happens to assign more than one label to each vertex. The output file is a FreeSurfer 'overlay' format file, in which each vertex has an associated value, in this case the count of labels assigned to that vertex. This can be displayed in tksurfer as a color. Setting fthresh to 1.5 will distinguish good vertices (count<=1) from bad (count>=2). |
Advanced |
--nocheckopts |
|
checkoptsonly = 0 |
XXXXXXXXXXXXX |
|
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
Methods Description
description description
References
["References/Lastname###"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>