<> '''Index''' <> = Name = '''mris_ca_train''' - Creates a cortical parcellation atlas file based on one or more annotated subjects. mris_ca_train builds probabilistic information estimated from a manually labeled training set (of annotated subjects). Note that an "annotation" is synonymous with a "parcellation", and is used for backwards compatibility. The manual labeling can be carried out directly on surface models using drawing tools in tksurfer, or volumetrically, then sampled onto the surfaces using [[mris_sample_parc]]. This information is then used by [[mris_ca_label]] to automatically assign 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 the training set. The result of mris_ca_train and mris_ca_label is a complete labeling of cortical sulci and gyri. = Synopsis = mris_ca_train [options] [subject2 ...] = Arguments = == Positional Arguments == || [options] || -sdir, -nbrs, -orig, -norm1, -norm2, -norm3, -ic, -sulc, -sulconly, -a, -t, -v, -n, --help, --version || || || hemisphere: rh or lh || || || Name of canonical surface file to input from every subject, usually lh.sphere.reg or rh.sphere.reg || || || Name of per-subject annotation file to input from every subject, eg: lh.my_manual_labeling.annot|| || [subject 2...] || subject(s) || || || classifier array output file, eg: ./lh.my_atlas.gcs || == Required Positional Arguments == hemi canonsurf annotfile subject1 outputfile == Optional Flagged Arguments == || -sdir || specify a subjects directory (default=$SUBJECTS_DIR) || || -nbrs || neighborhood size (default=2) || || -orig || specify filename of original surface (default=smoothwm) || || -norm1 || GCSA normalize input #1 after reading (default: disabled) || || -norm2 || GCSA normalize input #2 after reading (default: disabled) || || -norm3 || GCSA normalize input #3 after reading (default: disabled) || || -ic || parameters passed to the classifier routine (default: -ic 7 4) || || -sulc || specify sulc as only input (default: sulcus and curvature) || || -sulconly || same as -sulc || || -a || number of averages (default=5) || || -t || specify parcellation table input file (default: none) || || -v || diagnostic level (default=0) || || -n || number of inputs (default=1) || || --help || print help info || || --version || print version info || = Outputs = || || classifier array output file, containing probabilistic information estimated from the manually labeled training set || = Example = {{{ mris_ca_train -n 2 \ -t ./my_color_file.txt \ lh \ sphere.reg \ my_manual_labeling \ $SUBJECTS \ ./lh.my_atlas.gcs }}} In this example, mris_ca_train would look for an annotation file named '''lh.my_manual_labeling.annot''' in each of the subjects listed in $SUBJECTS label dir (e.g. $SUBJECTS_DIR/$s/label), and also assumes that a canonical surface file named '''lh.sphere.reg''' exists in the surf dir of each subject. An annotation file is created in tksurfer. See wiki pages [[tksurfer_labeledit]] or [[TkSurferGuide/TkSurferWorkingWithData/TkSurferLabel|TkSurferLabel]]. '''File->Label->Export Annotation''' is what exports all labels that have been assigned to a structure into the .annot file. To make assignments, open the 'Labels' window, via '''View->Windows->Labels''', and assign each label to a structure and it's associated color. If you want to modify the set of available structures (and their colors), then you should create a new file in the same format as $FREESURFER_HOME/FreeSurferColorLUT.txt and select '''File->Lable->Load Color Table'''. The '''-n 2''' option tells it to use two feature dimensions for classification: curv and sulc (which is what is used by default). The '''-t ./my_color_file.txt''' option will read in the file '''my_color_file.txt''' and embed it in the atlas, so that mris_ca_label will put it in the automatically generated .annot files, so that later, tksurfer (and other things) can read it in. The format of the '''my_color_file.txt''' file consists of a set of lines like: {{{ 0 unknown 1 1 1 0 1 oasis.chubs.ifc 25 100 40 0 }}} The first line is a 'default' label, that must be named 'unknown', that must be included in the colortable when creating a .annot file when mris_label2annot was run. It will be the label for any vertex not labelled by one of the other labels. The second line in this colortable is an example of a valid label. The numbers are RGBA (red, green, blue, alphas) codes, where alpha is not used. Note that 'unknown' must have a non-zero color (ie cannot be 0 0 0 0). = Bugs = None = See Also = [[mris_sample_parc]], [[mris_ca_label]], SurfaceRegAndTemplates = 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 = Author/s = BruceFischl