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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''' - 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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|| <canonsurf> || canonical surface file || | || <canonsurf> || canonical surface file. Ie: the name of the spherical surface file which descibes the registration of a subject's vertices to the reference "average" surface. Example: sphere.reg || |
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|| <outputfile> || annotated surface output file || | || <outputfile> || annotated surface output file. Ie: an annotation file listing the region label for each vertex. See LabelsClutsAnnotationFiles|| |
Navigation(children) Index TableOfContents
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 descibes 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) |
-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
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>