CARET instructions for Windows


Open a Caret

File : Set Current Directory : Navigate to the correct directory : OK

File : Open Data File : File type = Volume Anatomy Files

            - Select the desired anatomy file – Open

            - Would you like to create a spec file? – No


Cropping the full anatomy to one hemisphere:

Volume : Resize Underlay Volume

            - Using the Horizontal view, set the X and Y min and max values

            - The X min value cannot be on the midline of 89

(left hem = at least 90 ; right hem = at least 88)

            - Write down these 4 values before pressing OK

(they are not save anywhere in case you need to crop again for any reason)

            - Press OK


            - Change to the Parasagittal view to set the Z min and max values

            - Write down these values too

            - Press OK

Press R to reset the crosshairs back to the AC origin

Volume : Edit Volume Attributes : Data tab : Rescale - Voxels : Output Range : Set button :

Byte – unsigned - OK – OK – Apply – Close

File : Save Data File : File type = Volume File – AFNI (*.HEAD)

            - Change name to reflect cropped hem (e.g. ... LEFT_HEM+orig.HEAD)

            - Volume type = Anatomy

            - Press Save

Would you like to create a spec file? – Yes

Create Spec File : Species = Human   Subject = “case identifier”   Hemisphere = “left or right”

                              Space = 711-2B   Category = INDIVIDUAL

Press OK

Accept the default spec file name – OK


Initial Segmentation:

Volume : SureFit Operations : Next >   Next >

            - Volume Selection : Volume Type = Anatomy   Volume File = “the one you just saved”

            Next >   Next >   

Next >  Set Histogram peaks to desired levels

            (Gray Peak – left peak – lower #   White peak – right peak – higher #)

Next >  Deselect the following boxes:

            - Generate Very Inflated Surface

            - Generate Ellipsoidal Surface

            - Generate Curvature, Depth and Paint Attributes

Next >   OK on Information pop-up


Initial Segmentation is started – this process will take a while.

When initial segmentation is complete:

Close ‘SureFit Operations’ dialog box

In main window : Switch to Volume view

Open D/C : Overlay/Underlay – Volume

            - Settings tab : deselect ‘Show Crosshairs’


Correcting handles :

Volume : Segmentation : Edit Voxels

            - correct handles by turning voxels on or off

            - when satisfied with your corrections …

Check for remaining handles :

Volume : Segmentation : Find Handles

            - Select X, Y and Z

            - Press ‘ Search for Handles’ button


If a handle is found, click on the line giving the coordinates of the handle in the ‘Handles’ box

This will make the volume jump to the view and slice containing the handle

It will show what is causing the handle

Fix the handle(s) – Then search for handles again


If no handles found – Press OK

File : Save Data File : File type = Volume File – AFNI (*.HEAD)

            - Volume type = Segmentation

            - Volume file = Segment_ErrorCorrected

            - Change File name to reflect completion (e.g.:Human…L.Corrected+orig.HEAD)

            - Press Save

Volume : SureFit Operations : Next >   Next >

            - Volume Selection : Volume Type = Segmentation 

          Volume File = Segment_ErrorCorrected (the one just saved)

            Next >   Next>  

            - Deselect Automatic Error Correction

            - Select Generate Very Inflated Surface, Ellipsoidal Surface, Curvature, Depth and Paint

            Next >   OK on Information pop-up

            - Leave everything deselected on Partial Hem Padding (unless needed)

            - Press OK


Final Segmentation Started


When Final Segmentation is complete:


Switch D/C to Overlay/Underlay – Surface

Underlay : Shape : Folding

Surface : Flatten Full or Partial Hem…

            - Flattening Type : Full Hemisphere (Ellipsoid) & Morph Sphere

            - Border Template Cuts : Select Human (hem) Standard Cuts

            - Press OK

When the Compressed Medial Wall surface shows up :

Move the ‘Continue Flattening Full Hemisphere’ pop-up box to the side of the Main Window


Reference for “official” border drawing tips


D/C : Page Selection : Border

-       Change Border Line Width / Point Size from 2.0 to 3.0

D/C : Page Selection : Overlay/Underlay – Surface

            - Switch Shape to Folding and select the Primary Overlay radio button

Layers : Borders : Delete Border with Mouse

            - Click on the Medial Wall and the Calcarine cut

Window : Viewing Window 2 : should be showing the Volume model

-       D/C : Overlay/Underlay – Volume : Selection tab : Segmentation – ‘Corrected+orig’

-       Switch viewing window 2 volume to the Coronal view

-       Scroll through until you find the posterior end of the Hippocampus – where it first opens

-       Click on the Medial edge of the ventral portion of the Hippocampus – so that the vertical (Parasagittal) cross-hair is even with it

-       Then move the vertical cross-hair laterally 12 mm and click on where that intersects the segmentation

-       Repeat this every 4 to 5 slices creating a guideline of highlighted nodes on the Compressed Medial Wall surface where your new Medial Wall should be drawn

-    Do this until 12 mm puts you within the segmentation portion

-    Switch viewing window 2 model to the INFLATED surface Medial view

-     Continue to highlight nodes identifying the correct Medial Wall

In the Main Window, zoom up on the CMW surface so the highlighted MW fills up the window

Layers : Borders : Draw Borders

            - Name : Select : MEDIAL.WALL : Apply – draw along id points in main window

                        - left click to complete border

Go back to the Viewing Window 2 and highlight nodes where the Calcarine cut should be

            In the Draw Borders pop-up box:

            - Name : Select : CalcarineCut : Apply – draw along id points in main window

                        - left click to complete border

                        (make sure it crosses the Medial Wall border)

Layers : Borders : Project Borders : OK

(Can use Layers : Borders : Move Borders Point with Mouse if you are unhappy with any   particular area of  borders, instead of having to draw the entire thing again – if you do move any border points, make sure to project borders again before saving)


File : Save Data File : File type = Border Projection Files

            - File name : change to … BORDERS_forFlattening…borderproj

                        (this is just in case something goes wrong with flattening you have a backup)


Press ‘Continue Flattening’ button on Flattening dialog box

When Initial Flattening dialog box pops up, check the Initial Flat surface to make sure there

            are no major ‘blemishes’

Press ‘Continue Flattening’ if the surface looks good

Press OK on both pop-up boxes


Flattening is started – this process takes a little time


When flattening is complete:

Move ‘Align Surface(s) to Standard Orientation’ dialog box to the side

Make sure the number of crossovers on both the Spherical and Flat Morphing boxes is under 25

Press OK on both boxes

Viewing Window 2 : Change to Inflated surface – Lateral view

ID the ventral tip of the Central Sulcus

In main window - Click on the ventral tip of the Central Sulcus – ID point just marked

                           - Shift-click on the dorsal tip of the Central Sulcus

Accept all other defaults

Press Apply

File : Save Data File : File Type = Coordinate Files

            - Change name to … FLAT_CARTESIAN.(node #).coord

            - Save

Switch to SPHERE_CYCLE4 surface

File : Save Data File : File Type = Coordinate Files

            - Change name to … SPHERICAL.Std.(node #).coord

            - Save

File : Save Data File : File Type = Latitude Longitude Files

            - Change name to …(hem).LAT-LONG.(node #).latlon


Switch to FIDUCIAL surface – Medial view

Surface : Measurements : Generate Curvature

            - Select Folding for Folding and Gaussian Curvature for Gaussian Curvature

            - OK


File : Save Data File : File Type = Surface Shape Files

            - Change name to …(hem).(node #).surface_shape

            - Save


Clean up Spec File:

Press Spec button : Press the X button by the following files:

            Coordinate Files: Raw, SPHERE_CYCLE4, SPHERE, Ellipsoidal, CMW,

                                         FLAT_CYCLE5 and InitialFlat

            Border Files: Template Cuts

            Border Projection Files: BORDERS_forFlattening

            Surface Shape Files: the old (long) one

Close Spec box

Quit Caret


Clean up Directory:

Get rid of the following files:

Raw.coord, TemplateCuts, flat and spherical_morph_distortion, coords_as_border, and all ‘CYCLE’ files



Double click on the Spec file to open a new Caret

In the Spec File box, Select : Coordinate Files : Inflated, Spherical and Flat

                                                Area Color and Paint file

- Load 

File : Open Data File : File Type = Border Color Files

            - Find ‘ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor’

            - Yes – Copy to current directory

D/C : Shape : Folding

Switch to Flat surface in the main window

Window : Viewing Window 2 : switch to Inflated surface – Lateral view

Click ID nodes for the beginning and end of the next three registration borders

- Central Sulcus (dorsal tip 18mm from medial edge – ventral tip 19mm from edge of            fold)

            - Sylvian Fissure  (on flat – 9mm posterior to intersection with secondary sylvian)

- SF_STSant (aka the pink one) (drop directly below ventral point of central on the inflated surface to the anterior most point of the surface)

Zoom in on the Flat surface (in Main Window) to draw most accurate landmark borders possible

Layers : Borders : Draw Border

            - Name : Select : Central Sulcus : OK : Apply

- draw from ventral point to dorsal point along sulcul line

            - Name : Select : Sylvian Fissure : OK : Apply

                        - draw from posterior point to anterior point

            - Name : Select : SF_STSant : OK : Apply

- draw from posterior point to anterior – dorsal to ventral on the flat surface


D/C : Border : Select ‘Show First Link Red’


Layers : Borders : Project Borders : Nearest Tile : OK

Move border points if necessary to make most accurate – if this is done, Project Borders again


File : Save Data File : Border Projection File :




Switch to INFLATED surface in the main window


Toolbar : Spec : Open : Border Projection File ‘LANDMARKS.FromFlattening’

            - Append borders

Tweak the borders from flattening :

Layers : Borders : Delete Border Point with Mouse

(Calcarine’s first point should be 24mm from posterior most point of the inflated surface)

(first point of the dorsal medial wall should be directly across from the gyrus rectus of the olfactory sulcus)

(where the dorsal and ventral medial wall and the calcarine borders all meet at the posterior medial wall, make sure they have a little space between them all)


File : Save Data File : File Type = Border Projection Files

            - Yes to replace the file to keep the same name

            - Save


Switch to SPHERICAL surface in main window

File : Save Data File : File Type = Border Files

            - Copy the name from the borderproj and paste it here

            - Change to … LANDMARKS.REG-with-Pop-ATLAS_Core6.SPHERE.(node #).border

            - Make sure Sphere is indicated at the bottom

            - Save


Press Spec button – Click X button for Border Projection : LANDMARKS.FromFlattening

            - Close



Surface : Deformation : Run Spherical Surface Deformation

            - Individual tab : Spec File … : open the individual’s spec file

                                        Border File … : select the borderproj file (not the border file)

            - Atlas tab : Spec File : Navigate to Atlas directory : open ‘Reg-with-Individual’ spec

            - Spherical Parameters tab : Read Params from Def Map File : Navigate to Atlas

  directory : select ‘TEMPLATE_REG-with-POP-AVG_4k_NoFid.deform_map’

- Deformation tab : change prefix name if desired

- Press OK

Registration started

Press OK when deformation has completed