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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||<^> <CTabFile> ||<^>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||<^> <LabelFile> ||<^>LabelFiles[nlabels] = pargv[0][[BR]][[BR]]Repeat this flag and arg for each additional label file you want to include in the annotation file.[[BR]]||
||<^>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||<^> <AnnotName> ||<^>output annotation file The actual file will be called ""hemi.AnnotName.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||
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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

<CTabFile>

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

<LabelFile>

LabelFiles[nlabels] = pargv[0]BRBRRepeat this flag and arg for each additional label file you want to include in the annotation file.BR

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||<^> <AnnotName> ||<^>output annotation file The actual file will be called ""hemi.AnnotName.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

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

mris_label2annot (last edited 2017-12-20 11:54:21 by BramDiamond)