text: Foci and the PALS Atlas
  
  To successfully view foci on the PALS atlas, each focus MUST be linked to a study. Each of the studies MUST have a valid stereotaxic space. Studies are entered by using Attributes Menu->Study Metadata->Edit Studies. After studies are entered, the Study Metadata File must be saved. After foci are entered, the foci projection file must be saved.
  
  Press the Save button and chooseNo when asked if you would like to create a Spec File.
  
  Quit Caret.
  
  Opening the Foci File in Excel
  
  The steps below describe how to read, edit, and save the spreadsheet foci file in the Mac OSX version of Excel.
  
  In Excel, selectFile Menu->Open.
  
  In the Open Dialog, setEnable to All Documents.
  
  Select the file that was created in Caret and press the Open button.
  
  In the Text Import Wizard, selectDelimited in the Original Data Type section. Press the Next button.
  
  On the Text Import Wizard Step 2 of 3 page, change the Delimiters so that only Comma is selected. Press the Next button.
  
  Press the Finish button.
  
  Editing the Foci in Excel
  
  As needed, add additional rows to the spread sheet for each focus in the area between the row with all of the data column titles (Cell Number, X, Y, Z, etc) and the row that begins with csvf-section-end. Do not alter any of the column titles (X, Y, Z, section,etc). Otherwise, Caret will be unable to read the file.
  
  Several fields MUST be entered for each focus. These fields are:
  
  X
  
  Y
  
  Z
  
  Name
  
  Study PubMed ID
  
  The "Study PubMed ID" should be set to the identifier assigned by [http://www.pubmed.gov]. If this data is unpublished or the PubMed ID is not available, enter a Project ID in the Study PubMed ID column. To get a Project ID, you will need to create a study in Caret (Layers Menu->Study Metadata->Edit Studies. Each new study created in Caret is automatically assigned a unique Project ID. If the foci will be projected to the PALS atlas, the study must have a valid stereotaxic space.
  
  Saving the Spreadsheet in Excel
  
  SelectFile Menu->Save As.
  
  Set the Format to CSV (Windows).
  
  Enter a name different than the name of the file created in Caret, say "foci_test.csv.foci".
  
  Press the Save button.
  
  PressNo on the "features not compatible" message dialog.
  
  Reading the Foci Into Caret
  
  SelectFile Menu->Open Data File.
  
  Set the File Type to Foci File.
  
  Select the file you saved in Excel (Sometimes Excel adds "csv" onto the end of the filename).
  
  Press the Open button.
  
  SelectLayers Menu-Project Foci to PALS Atlas and press the OK button. If you get a message that a stereotaxic space is missing, verify that the foci are linked to studies with valid stereotaxic spaces.
  
  Save the Study Metadata, Foci Projection, and Foci Color Files.
  
  To set the colors of the foci, use Layers Menu->Foci->Edit Foci Colors.
  
  Map Stereotaxic Foci Dialog
  
  Foci are added and edited using the Map Stereotaxic Focus Dialog. After making any changes to entered values, the Apply button must be pressed.
  
  Automatic Projection of Foci Section
  
  Automatic projection is selected by default. If the foci are to be projected to the fiducial surface in the main window, select the Main Window Surface radio button. If the foci are to be projected to the PALS atlas, check the PALS Atlas Surface in Correct Stereotaxic Space button.
  
  Projection to PALS Atlas
  
  To project foci to the PALS atlas, the surface(s) loaded must be PALS surfaces (73730 nodes). In addition, the Study Metadata link must be set to a study with a valid, PALS supported, stereotaxic space. The stereotaxic space is used by the projection algorithm to determine the accurate projection of the foci.
  
  During projection to the PALS atlas, some foci are located in the region between the cerebellum and ventral occipitotemporal cortex. To make this determination, a ratio of the distance to the nearest cerebral cortex over the distance to the cerebellum is calculated. If this ratio is less than the cerebral cutoff (default=2.0), the focus is assigned the left or right cerebral cortex. If the ratio is greater than the cerebellum cutoff (default=4.0), the focus is assigned to the cerebellum. If the ratio is between the cerebral and cerebeullum cutoffs, the focus is duplicated and placed in the foci projection file twice, once as cortex-left-or-cerebellum and once as cerebellum-or-cortex-left (similar for right cerebral hemisphere).
  
  The table below indicates when foci are displayed based upon the the structure to which the focus projected (the left-most column), the status of the Correct Structure Only option on the Display Control's Foci Main page (second row from top), and the surface that is displayed (top row).
  
  Focus/Surface
  
  Left
  
  Left
  
  Right
  
  Right
  
  Cerebellum
  
  Cerebellum
  
  Correct Structure Only
  
  On
  
  Off
  
  On
  
  Off
  
  On
  
  Off
  
  Left
  
  Y
  
  Y
  
  N
  
  Y
  
  N
  
  N
  
  Right
  
  N
  
  Y
  
  Y
  
  Y
  
  N
  
  N
  
  Cerebellum
  
  N
  
  N
  
  N
  
  N
  
  Y
  
  Y
  
  Left-or-Cerebellum
  
  Y
  
  N
  
  N
  
  N
  
  N
  
  N
  
  Right-or-Cerebellum
  
  N
  
  N
  
  Y
  
  N
  
  N
  
  N
  
  Cerebellum-or-Left
  
  N
  
  N
  
  N
  
  N
  
  Y
  
  N
  
  Cerebellum-or-Right
  
  N
  
  N
  
  N
  
  N
  
  Y
  
  N
  
  Focus Mode Section
  
  Adding Foci
  
  When adding foci, select the Add radio button. Enter the information about the focus and press the Apply button.
  
  Editing Foci
  
  Select the Edit Number radio button and enter the number of the focus. Make the desired changes and press the Apply button.
  
  An easier way for editing a focus is to place the mouse over the desired focus in the Main Window, click the right mouse button (control-click on Mac OSX), and select Edit Focus Under Mouse from the pop-up menu. The Map Stereotaxic Focus Dialog will appear with the focus selected for editing.
  
  Deleting Foci
  
  Select the Edit Number radio button, enter the number of the focus, and press the Delete button.
  
  An easier way to delete a focus is to place the cursor over the focus in the Main Window, right click the mouse (control-click on Mac OSX), and select Delete Focus Under Mouse from the pop-up menu.
  
  Focus Data Section
  
  Name - Name of the focus
  
  Class - The "class"; sometimes the table subheader's name.
  
  Position - The stereotaxic position of the focus with units in millimeters.
  
  Study in Focus File - Obsolete way of associating with study information in the foci file (DO NOT USE).
  
  Study Metadata - Link the focus to a study in the Study Metadata File. If projecting to the PALS atlas, this value must be a valid link to a study in the Study Metadata File with a valid stereotaxic space.