Index TableOfContents
Note: As of 2008-01-19, it looks to me like parts of this file were left-overs from the page of some unrelated command. I have moved these sections to the bottom "Obsolete?" section. Someone official can perhaps clean this up. -- GW
Name
mri_annotation2label - Converts annotation into label files
Synopsis
mri_annotation2label [Flagged arguments]
Arguments
Flagged Arguments
Category |
Flag |
<Args> |
Reqd |
Description |
Input |
--a2005s |
|
n |
Use 'aparc.a2005s' as the annotation base name, (Default: use 'aparc') |
Input |
--annotation |
<annotation> |
Y |
Selects input annotation file, as found in SUBJDIR/labels. Default is 'aparc'. |
Input |
--hemi |
<hemi> |
Y |
lh or rh. Used in conjunctions with surface name to compose surface file name. [Might be used with annotation name too? Not sure -- GW] |
Input |
--subject |
<subject> |
Y |
source subject |
Input |
--surface or --surf |
<surfacename> |
n |
Name of surface. Default if omitted: 'white'. This selects the surface file that the program will read in order to create R,A,S coordinates for each vertex listed in a label file. |
Input |
--table |
|
n |
ERROR: Older versions of program worked in conjunction with separate colortable. Current versions expect to read colortable from annotation file. |
Output |
--border |
<borderfile> |
n |
Creates an overlay file in which the boundaries of the parcellations are set to 1 and everything else is 0. This can then be loaded as an overlay in tksurfer. |
Output |
--labelbase |
<labelbase> |
n |
If supplied, the program will compose output label filenames using the pattern 'labelbase-XXX.label' (where XXX is label number). (Default: compose label filenames based on label names found in annotation file.) |
Output |
--outdir |
<outdir> |
? |
Directory in which to place output label files. Complete path will be: 'outdir/hemi.name.label' (with 'name' composed according to other rules). Required unless specifying one of the other kinds of output. |
Output |
--seg |
<segfile> |
n |
This option causes program to output a 'volume-encoded surface segmentation file'. This is simply the list of per-vertex label values (count = count of vertices), dumped into a file whose format looks like an FS volume file... which some other FS programs are equipped to load. (Ie: it is not actually volume data). See details below. |
Output |
--segbase |
<segbase (int)> |
n |
Add segbase to each label value when outputting to a segfile. |
Utility |
--debug |
|
n |
enable debugging options |
Utility |
--help |
|
n |
display help |
Utility |
--version |
|
n |
display version |
XXXXXXXXXXXXX |
|
- |
Description
This program will convert an annotation file into multiple label files. Inputs are specified via subject, hemisphere, and optionally, if defaults are not wanted, a base name for the annotation, and a specific surface to be used for the R,A,S coordinates to be placed in the label files.
- By default, the base name for the annotation file is 'aparc', so that the actual input annotation file is SUBJECTS_DIR/subject/label/lh.aparc.annot or rh.aparc.annot.
- A separate label file is created for each annotation index.
- The output file names can take one of two forms:
- If --outdir dir is used, then the output will be dir/hemi.name.label, where 'name' is the corresponding name in
the lookup table in the annotation file.
If --labelbase is used, name of the file is composed using the pattern: labelbase-XXX.label, where XXX is the zero-padded 3 digit annotation index. (I assume that "annotation index" means label value. Not sure what happens for label values > 999. --GW) If labelbase includes a directory path, that directory must already exist.
- If there are no points in the annotation file for a particular index, no label file is created.
- The xyz (R,A,S) coordinates in the label file are obtained from the values at that vertex of the specified surface. The default surface is 'white'. Other options include 'pial' and 'orig'.
Probably applies to obsolete version
The human-readable names that correspond to the annotation indices for aparc depend upon how the annotations were created. They are created with the program mris_ca_label, and the human readable names are in the file given as the argument to the -t flag. Unfortunately, this information is not maintained inside the annotation file, and it must be supplied to mri_annotation2label through the --table flag.
Examples
Example 1
mri_annotation2label --subject LW \ --hemi rh \ --labelbase ./labels/aparc-rh
This will get annotations from $SUBJECTS_DIR/LW/label/rh_aparc.annot and then create about 94 label files: aparc-rh-001.label, aparc-rh-002.label, ... Note that the directory 'labels' must already exist.
Example 2
mri_annotation2label --subject LW \ --hemi rh --outdir ./labels
This will do the same thing as above except that the output files will have names of the form lh.S_occipital_anterior.label
Bugs
If the name of the label base does not include a forward slash (ie, '/') then the program will attempt to put the label files in $SUBJECTS_DIR/subject/label. So, if you want the labels to go into the current directory, make sure to put a './' in front of the label base.
Testing
- Start tksurfer:
- tksurfer -LW lh inflated read_annotations lh_aparc
- When a point is clicked on, it prints out a lot of info, including something like:
- annot = S_temporalis_sup (93, 3988701) (221, 220, 60)
- Start another tksurfer and load the label:
- tksurfer -LW lh inflated [edit label field and hit the 'Read' button]
- Verify that label pattern looks like the annotation as seen in the tksurfer window from step 1.
- Load label into tkmedit
- tkmedit LW T1 [Load the label]
- [Goto the point saved from step 1]
See Also
Obsolete?
Positional Arguments
Required Flagged Arguments
--srcreg |
srcreg.dat |
--targreg |
targreg.dat |
Optional Flagged Arguments
--targsubj subjid |
default is talairach |
--xfm xfmrname |
xfm file name relative to transforms |
--sd subjects_dir |
default is env SUBJECTS_DIR |
--fvol funcvol |
path to example functional volume |
--help |
|
--version |
Positional Arguments
Required Flagged Arguments
--srcreg |
srcreg.dat |
--targreg |
targreg.dat |
Optional Flagged Arguments
--targsubj subjid |
default is talairach |
--xfm xfmrname |
xfm file name relative to transforms |
--sd subjects_dir |
default is env SUBJECTS_DIR |
--fvol funcvol |
path to example functional volume |
--help |
|
--version |
Links
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>