Differences between revisions 6 and 7
Deletions are marked like this. Additions are marked like this.
Line 19: Line 19:
|| <outputfile> || outputfile || || <outputfile> || annotated surface output file ||

Navigation(children) Index TableOfContents

Name

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"]).

Synopsis

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

Arguments

Positional Arguments

[options]

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

<subject>

subject id

<hemi>

hemisphere: rh or lh

<canonsurf>

canonical surface file

<classifier>

specify classifier array input file

<outputfile>

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)

-long

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

-r <filename>

file containing precomputed parcellation

-novar

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

-u

same as -?

--help

print help info

--version

print version info

Outputs

outputfile

labeled cortical surface model

Example

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

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.

Bugs

none

See Also

["mris_sample_parc"] ["mris_ca_train"]

Links

CorticalParcellation, FreeSurfer, FsFast

References

[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>

Author/s

BruceFischl

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