Name

mris_ca_label - For a single subject, produces an annotation file, in which each cortical surface vertex is assigned a neuroanatomical label.

This automatic procedure employs data from a previously-prepared atlas file. An atlas file is created from a training set, capturing region data manually drawn by neuroanatomists combined with statistics on variability correlated to geometric information derived from the cortical model (sulcus and curvature). Besides the atlases provided with FreeSurfer, new ones can be prepared using 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. Ie: the name of the spherical surface file which describes the registration of a subject's vertices to the reference "average" surface. Example: sphere.reg
<classifier>	specify classifier array input file
<outputfile>	annotated surface output file. Ie: an annotation file listing the region label for each vertex. See LabelsClutsAnnotationFiles

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)

|| -p <filename> || output a file containing label probability for each vertex (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

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 → 
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+   ← Revision 15 as of 2013-11-11 12:35:41 → ⇥
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  Comment:
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[[Navigation(children)]]
+<<Navigation(children)>>
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-[[TableOfContents]]
+<<TableOfContents>>
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-mris_ca_label
+'''mris_ca_label''' - For a single subject, produces an annotation file, in which each cortical surface vertex is assigned a neuroanatomical label.  

This automatic procedure employs data from a previously-prepared atlas file. An atlas file is created from a training set, capturing region data manually drawn by neuroanatomists combined with statistics on variability correlated to geometric information derived from the cortical model (sulcus and curvature).  Besides the atlases provided with FreeSurfer, new ones can be prepared using [[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. Ie: the name of the spherical surface file which describes the registration of a subject's vertices to the reference "average" surface. Example: sphere.reg ||
|| <classifier> || specify classifier array input file ||
|| <outputfile> || annotated surface output file. Ie: an annotation file listing the region label for each vertex. See LabelsClutsAnnotationFiles||
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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) ||
|| -p <filename> || output a file containing label probability for each vertex (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]], SurfaceRegAndTemplates
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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