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| This command-line program amalgamates one or more label files, plus optionally a color lookup table, into a single annotation file. | This command-line program amalgamates one or more label files, plus optionally a color lookup table, into a single annotation file. The concepts relating to label files and annotation files are described here: LabelsClutsAnnotationFiles. |
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| command argA argB -flag1 arg1 -flag2 arg2 [-flag3 arg3] [-flag4 arg4] | mris_label2annot [Flagged args, see below] |
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= Outputs = || volume1 || description || || volume2 || description || |
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| command foo -i f -o out |
The following example is taken from mris_label2annot's help --GW {{{ mris_label2annot --s bert --h lh --ctab aparc.annot.ctab --a myaparc --l lh.unknown.label --l lh.bankssts.label --l lh.caudalanteriorcingulate.label --nhits nhits.mgh }}} |
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| description |
This will create lh.myaparc.annot in bert/labels using the three labels specified. Any vertices that have multiple labels will then be stored in nhits.mgh (as a volume-encoded surface file). |
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== Example 2 == command foo -i f -o out -f fvalue |
(Note: this nhits.mgh detail is a bit obscure. The idea of an nhits file is simply to provide a list of values giving the count of labels found for each vertex. This needs to be presented to tksurfer for display as a colored overlay. Here FS's MRI volume format is used just as a container for that 1 x VertexCount array of values. --GW) |
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| description |
To view, run: tksurfer bert lh inflated -overlay nhits.mgh -fthresh 1.5 Then File->Label->ImportAnnotation and select lh.myaparc.annot. |
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| ["mri_annotation2label"], ["othercommand2"] | ["mri_annotation2label"], LabelsClutsAnnotationFiles |
Index TableOfContents
mris_label2annot
This command-line program amalgamates one or more label files, plus optionally a color lookup table, into a single annotation file. The concepts relating to label files and annotation files are described here: LabelsClutsAnnotationFiles.
Synopsis
mris_label2annot [Flagged args, see below]
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 |
|
Description
This program is used to amalgamate one or more label files together into a single annotation file, usually including a color lookup table file. The concepts relating to label files and annotation files are described here: LabelsClutsAnnotationFiles.
Examples
Example 1
The following example is taken from mris_label2annot's help --GW
mris_label2annot --s bert --h lh --ctab aparc.annot.ctab --a myaparc --l lh.unknown.label --l lh.bankssts.label --l lh.caudalanteriorcingulate.label --nhits nhits.mgh
This will create lh.myaparc.annot in bert/labels using the three labels specified. Any vertices that have multiple labels will then be stored in nhits.mgh (as a volume-encoded surface file).
(Note: this nhits.mgh detail is a bit obscure. The idea of an nhits file is simply to provide a list of values giving the count of labels found for each vertex. This needs to be presented to tksurfer for display as a colored overlay. Here FS's MRI volume format is used just as a container for that 1 x VertexCount array of values. --GW)
To view, run: tksurfer bert lh inflated -overlay nhits.mgh -fthresh 1.5 Then File->Label->ImportAnnotation and select lh.myaparc.annot.
Bugs
None
See Also
["mri_annotation2label"], LabelsClutsAnnotationFiles
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>