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, --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)
--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

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

-  ⇤ ← Revision 1 as of 2004-08-27 08:47:09 → 
  Size: 967
  Editor: KatyThakkar
  Comment:
+   ← Revision 10 as of 2005-12-05 20:20:06 → ⇥
  Size: 2889
  Editor: NickSchmansky
  Comment: removed -? option
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+Additions are marked like this.
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## using the latest version of the CommandTemplate
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-mris_ca_label
+'''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"]).
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-mris_ca_label <subject> <hemi> <canon surf> <classifier> <output file>
+mris_ca_label [options] <subject> <hemi> <canonsurf> <classifier> <outputfile>
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-|| subject || subject ||
|| hemi || hemisphere ||
|| canon surf ||
|| classifier ||
|| output file||
+|| [options] || -sdir, -orig, -long, -novar, -nbrs, -f, -v, -w, -r, --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 ||
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+subject hemi canonsurf classifier outputfile
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+|| -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) ||
|| --help || print help info ||
|| --version || print version info ||
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+|| outputfile: || labeled cortical surface model ||
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-= Description =


= Examples =
+= 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.
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-None
+none
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+["mris_sample_parc"], ["mris_ca_train"]
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-FreeSurfer, FsFast

= Methods Description =
+CorticalParcellation, FreeSurfer, FsFast
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+[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.
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+BruceFischl