<> '''Index''' <> = Name = '''mris_sample_parc''' - Samples a volumetric parcellation onto a surface. Manual labeling can be carried out directly on surface models using drawing tools in tksurfer, or volumetrically in tkmedit, then sampled onto the surfaces using mris_sample_parc. [[mris_ca_train]] is used to create an atlas from a set of annotated subjects. The information output by [[mris_ca_train]] is then used by [[mris_ca_label]] to automatically assign a neuroanatomical label to each location on a cortical surface model. Note that an "annotation" is synonymous with a "parcellation", and is used for backwards compatibility. = Synopsis = mris_sample_parc [options]

= Arguments = == Positional Arguments == || [options] || -u, -t, -w, -a, -f, -v, -ct, -file, -projfrac, -projmm, -proj, -trans, -replace, -fix, -surf, -sdir, --version, --help || || || the subject id || || || hemisphere: rh or lh || || || parcellation filename || ||

|| annotation filename || == Required Flagged Arguments ==

== Optional Flagged Arguments == || -sdir || use as subjects directory (default: $SUBJECTS_DIR)|| || -surf || use as surface (default: 'white') || || -fix || fix topology of all labels smaller than vertices (default=-1, do all)|| || -replace || replace label with deeper ones || || -trans || translate to || || -projmm || project millimeters along surface normal (default=0.0) || || -proj || same as -projmm || || -projfrac || project percent along surface normal (default=0.5) || || -file || use as translation (default: 'cma_parcellation_colors.txt')|| || -ct || embed color table into output annotation file || || -v || diagnostic level (default=0) || || -f || apply mode filter times to parcellation (default=0) || || -a || smooth surface times (default=0) || || -w || use window size for sampling (default=7) || || -t || use thickness file (default: 'thickness') || || -u || change largest connected unknown region to label (default: don't change) || || --help || print help info || || --version || print version info || = Outputs = ||

|| parcellation annotation output file || = Example = {{{ mris_sample_parc -ct FooColorLUT.txt subject01 lh subj01_parc_masks.mgz lh.parcmask.annot }}} This samples the volumetric parcellation `subj01_parc_masks.mgz` as an annotation `lh.parcmask.annot` for the subject `subject01's` left hemisphere. The output annotation is embedded with the [[LabelsClutsAnnotationFiles#head-e5ec66fee7ea903e9c03faa12cd076c541ad0a62|color table]] information in `FooColorLUT.txt` file, and is usually saved in `$SUBJECTS_DIR/$SUBJECT/label/` directory. = Bugs = None = See Also = [[mris_ca_train]] [[mris_ca_label]] = Links = CorticalParcellation, FreeSurfer, FsFast = References = = Reporting Bugs = Report bugs to = Author/s = BruceFischl