Software version described:


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.


mris_label2annot [Flagged args, see below]


Positional Arguments


Flagged Arguments






Colortable file. File that defines the structure names, their indices, and their color. This must have the same format as that found in $FREESURFER_HOME/FreeSurferColorLUT.txt.
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.



Repeat this flag and arg for each additional label file you want to include in the annotation file.



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


Works like --ldir option, setting labeldir to the default label directory for the selected subject:


--s or --subject


FreeSurfer subject to work on

--a or --annot


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.

--h or --hemi


hemisphere (lh or rh)


Start label numbering at index 0 instead of index 1. Do not map unhit vertices (ie, vertices without a label) to 0.






checkoptsonly = 1


debug = 1



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).


checkoptsonly = 0



Add to label number to get CTAB index.




Turn off overlap and stat override messages.


Keep label with highest 'stat' value.



threshold label by stats field.



Default is orig.


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.


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 vertex_count array of values. --GW)

To view, run: tksurfer bert lh inflated -overlay nhits.mgh -fthresh 1.5 Then File -> Label -> Import Annotation and select lh.myaparc.annot.



See Also

mri_annotation2label, LabelsClutsAnnotationFiles

Reporting Bugs

Report bugs to <>

Document Author/s


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