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mris_ca_label - Automatically assigns a neuroanatomical label to each location on a cortical surface model. This procedure incorporates both geometric information derived from the cortical model (sulcus and curvature), and neuroanatomical convention, as found in a training set (see ["mris_ca_train"]).


mris_ca_label [options] <subject> <hemi> <canonsurf> <classifier> <outputfile>


Positional Arguments


-sdir, -orig, -long, -novar, -nbrs, -f, -v, -w, -r, -?, -u, --help, --version


subject id


hemisphere: rh or lh


canonical surface file


specify classifier array input file


annotated surface output file

Required Flagged Arguments

subject hemi canonsurf classifier outputfile

Optional Flagged Arguments

-sdir <subject dir>

specify a subjects directory (default=$SUBJECTS_DIR)

-orig <filename>

specify filename of original surface (default=smoothwm)


refines the initial labeling read-in from -r (default: disabled)

-r <filename>

file containing precomputed parcellation


sets all covariance matrices to the identify (default: disabled)

-nbrs <number>

neighborhood size (default=2)

-f <number>

applies mode filter <number> times before writing output (default=10)

-t <filename>

specify parcellation table input file (default: none)

-v <number>

diagnostic level (default=0)

-w <number> <filename>

writes-out snapshots of gibbs process every <number> iterations to <filename> (default=disabled)


print usage info


same as -?


print help info


print version info



labeled cortical surface model


mris_ca_label \
 -orig white \
 -novar \
 -t $SUBJECTS_DIR/scripts/colortable_final.txt \
 my_subject \
 lh \
 sphere.reg \
 $SUBJECTS_DIR/average/lh.rahul.gcs \

In this example, mris_ca_label take sphere.reg as the canonical surface input file, lh.rahul.gcs as the classifier array input file, and writes the annotated surface info to lh.raparc.annot. The file colortable_final.txt is embedded into the output file, so that tksurfer (and other utilities) can read it in.



See Also

["mris_sample_parc"] ["mris_ca_train"]


CorticalParcellation, FreeSurfer, FsFast


[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Automatically Parcellating the Human Cerebral Cortex], Fischl et al., (2004). Cerebral Cortex, 14:11-22.

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>



mris_ca_label (last edited 2013-11-11 12:40:07 by MaritzaEbling)