I. SUMA (SUrface MApping)

A. Highlights:

1. Surface rendering with direct AFNI link:

2. Multiple Linked Viewers:

3. ROI Drawing:

4. Simultaneous left / right hemisphere display:

5. Talairach surface and volume:

6. Control of dataset color mapping (color plane) order and opacity:

7. Recording in continuous and single frame modes:

8. A set of command line programs for batch processing:

a. Volume to surface & surface to volume mapping:

b. Filtering:

c. Miscellaneous:

B. Test-drive

1. Nomenclature:

2. Showcase:

C. Setting up surfaces and volumetric data:

1. A- Surface Specification File:

a. In a nutshell:

b. The skinny:

i. Creating the specs file for FreeSurfer:

ii. Creating the spec files for SureFit:

2. B- Alignment of Surface to Experimental Data

a. In a nutshell:

b. The skinny:

3. C- Running SUMA

a. In a nutshell:

b. The skinny:

D. Interacting with SUMA

1. SUMA viewer title:

2. Viewer Menus:

a. File Menu:

i. Save View:

ii. Load View:

iii. Close:

b. View Menu:

i. SUMA Controller:

ii. Surface Controller:

iii. Viewer Controller:

iv. Cross Hair:

v. Node in Focus:

vi. Selected Faceset:

c. Tools Menu:

i. Draw ROI:

d. Help Menu:

i. Usage:

ii. Message Log:

iii. SUMA Global:

iv. Viewer Struct:

v. Surface Struct:

vi. InOut Notify:

vii. MemTrace:

3. Mouse Controls:

a. Button 1&Motion:

b. Button 2&Motion:

c. Button 1+2&Motion or Shift+Button2 & Motion:

d. Button 3-Press:

e. Shift+Button3-Press:

4. Keyboard Controls:

a. a : attenuation by background, toggle.

b. 'b': background color, toggle.

c. ‘B’: Backface culling, toggle.

d. 'c': node color file

e. ‘Ctrl+d’: draw ROI controller

f. 'F': Flip light position

g. 'f': functional overlay, toggle.

h. ‘H’: Highlights a set of nodes inside a box

i. ‘h’: No longer used, use ‘ctrl+h’ instead.

j. 'Ctrl+h': help message

k. ‘J’: Jump to faceset n on Surface Object (SO) in Focus.

l. ‘j’: jump to node n on SO in Focus

m. ‘Ctlr+j’: jump to XYZ location

n. ‘Alt+j’: jump to node n on SO in Focus.

o. ‘L’: Light’s XYZ coordinates.

p. 'l': look at point X,Y,Z

q. ‘Ctrl+l’: lock mode switch

r. ‘Alt+l’: look at crosshair location

s. 'm': momentum ON/OFF, toggle.

t. ‘Alt+Ctrl+M’: Dumps memory trace to file .

u. ‘Ctrl+n’: new SUMA viewer .

v. ‘p’: viewer rendering mode.

w. ‘r’: record the current image.

x. ‘R’: Record continuously, toggle.

y. ‘Ctrl+s’: open controller for surface in Focus.

z. ‘Alt+s’: switch function of mouse buttons 1 an 3.

aa. 't': talk to AFNI toggle.

bb. ‘Ctrl+t’: Force a resend of surfaces to AFNI

cc. ‘T’: Start listening for NIML connections

dd. ‘Ctrl+u’: open SuMA controller.

ee. 'w': write the rendered image.

ff. ’W’: Write the SO in Focus to disk.

gg. 'Z' / 'z': Zoom in out

hh. '*': Smooth node colors by averaging with neighbors.

ii. ‘8’: Set the number of smoothing iterations to the foreground.

jj. '.'/ ',' (period and comma): Switch to next/previous viewing state:

kk. ‘[‘/’]’ (left and right square brackets): show left / right hemispheres, toggle:

ll. SPACE: toggle to/from Mapping Reference State

mm. L-R arrows: rotate about screen's Y axis

nn. U-D arrows: rotate about screen's X axis

oo. Shift+L-R arrows: translate about screen's Y axis

pp. Shift+U-D arrows: translate about screen's X axis

qq. Ctrl+L-R arrows: LR cardinal views

rr. Ctrl+U-D arrows: IS cardinal views

ss. Ctrl+Shift+U-D arrows: AP cardinal views

tt. F1: object axis, toggle

uu. F2: screen axis, toggle

vv. F3: cross hair, toggle

ww. F4: Node selection highlight, toggle

xx. F5: Facet selection highlight, toggle

yy. F6: set background color to 1 – color

zz. F7: Switch between color mixing modes.

aaa. F12: Time duration for 20 scene renderings

bbb. ‘Escape’: Close the surface viewer window

ccc. ‘Shft+Escape’: Close all surface viewer windows

ddd. HOME: reset view to startup setting

5. SUMA Controller:

a. Lock: controls for locking cross-hair and viewpoint across viewers

b. Viewer: opens a new viewer (just like ‘Ctrl+n’).

c. BHelp: Provides help for certain buttons.

d. Close: Closes the SUMA controller

e. done: Kills SUMA, no questions asked.

6. Surface Controller:

a. Surface Properties Block:

i. more:

ii. RenderMode:

iii. Dsets:

b. Xhair Info Block:

i. Xhr:

ii. Node:

iii. Tri:

iv. Node Values Table:

v. Node Label Table:

c. Dset Controls Block:

i. Dset Info Table:

ii. Ord:

iii. Opa:

iv. Dim:

v. view:

vi. 1 Only:

vii. Switch Dset (used to be Switch Col. Plane):

viii. Load Dset:

ix. Load Col:

d. Dset Mapping Block:

i. The Scale bar:

ii. The Colormap:

iii. I:

iv. v:

v. T:

vi. v:

vii. B:

viii. v:

ix. Mapping Parameters Table:

x. Col:

xi. Bias:

xii. Cmp:

xiii. New

xiv. |T|:

xv. sym I:

xvi. shw 0:

e. Data Range Table:

E. Viewer Controller

F. Color Planes:

G. Drawing ROIs:

1. Demo:

2. Usage:

a. Parent: Label of the surface on which the ROI is drawn.

b. Draw Mode: Toggles drawing mode.

c. Pen: Toggles pen drawing mode

d. Afni Link: If turned on, then ROIs drawn on the surface are sent to AFNI.

e. Label: Label of ROI being drawn.

f. Value: Integer value associated with ROI.

g. Undo: Multiple level undo of drawing actions

h. Redo: Multiple level redo the last drawing action

i. Join: Connect the first node of the ROI to the last node.

j. Finish: Mark ROI as finished.

k. Switch ROI: Allows you to switch between Drawn ROIs.

l. Load: Load ROIs from disk files

m. Delete ROI: Delete a drawn ROI.

n. Save: Save ROIs to disk

o. Close: Close Draw ROI window

3. Mapping from volume to surface domains:

4. Mapping from surface to volume domain:

H. Surface Models in Talairach Space:

1. Mapping Talairach-Space Volumetric Data:

2. Creating Talairach Space Surface Models:

I. Aligning SurfVol to ExpVol:

1. Aligning SurfVol to ExpVol using 3dVolreg:

2. Aligning SurfVol to ExpVol using 3dTagalign:

J. Creating AFNI datasets from other formats:

1. FSL-ANALYZE to AFNI:

K. Surface-Based Cross-Subject Analysis:

1. Creating Standard Meshes

2. Statistical Analysis On The Surfaces

L. Auxillary Programs:

1. 3dSurf2Vol:

2. 3dVol2Surf:

3. CompareSurfaces:

4. ConvertSurface:

5. CreateIcosahedron:

6. FS_read_annot:

7. inspect:

8. MakeColorMap:

9. MapIcosahedron:

10. quickspec:

11. ROI2dataset:

12. ScaleToMap:

13. SUMA_glxdino:

14. SurfMeasures:

15. SurfaceMetrics:

16. SurfSmooth:

17. SurfPatch:

18. SurfQual:

M. Communication between AFNI and SUMA:

1. Starting NIML connection:

2. AFNI to SUMA Communication:

3. SUMA to AFNI Communication:

II. Appendix A:

A. Surface Reconstruction Software:

B. File Formats:

1. 1D files:

2. 1D files as surface data sets:

3. NIML files:

4. Spec files:

a. Group:

b. FreeSurferSurface:

c. SurfaceName:

d. SurfaceVolume:

e. SureFitTopo:

f. SureFitCoord:

g. SureFitVolParam:

h. TopoFile:

i. CoordFile:

j. SurfaceFormat:

k. SurfaceType:

l. SurfaceState:

m. StateDef:

n. LocalDomainParent (LDP):

o. MappingRef (Obsolete, see LocalDomainParent):

p. EmbedDimension:

C. Environment variables:

1. SUMA_ArrowRotAngle:

2. SUMA_ColorPattern:

3. SUMA_SwapButtons_1_3:

4. SUMA_BackgroundColor:

5. SUMA_ROIColorMap:

6. SUMA_NumConvSmooth:

7. SUMA_ConvColorMap:

8. SUMA_ConvBrightFactor:

9. SUMA_NumForeSmoothing:

10. SUMA_ColorMixingMode:

11. SUMA_AFNI_TCP_PORT:

12. SUMA_WarnBeforeClose:

13. SUMA_MaskZero:

14. SUMA_AbsThreshold:

D. Colormaps:

III. Glossary

A. .afnirc:

B. @SUMA_AlignToExperiment:

C. @SUMA_Make_Spec_FS

D. @SUMA_Make_Spec_SF

E. Anatomically Correct Surfaces:

F. Axis Order:

G. Colormap generation:

H. Dsets (Surface Data Sets):

I. Experiment anatomy Volume (ExpVol):

J. Facet:

K. Homotopic or Topologically Isomorphic Surfaces:

L. IDcode:

M. Mapping Reference Surface (MapRef):

N. Node Datasets (Dsets):

O. Node Index or Node ID:

P. Nodes:

Q. Shell:

R. SRC:

S. Surface anatomy Volume (SurfVol):

T. SurfVol, Aligned to Experiment (SurfVol_AlndExp):

U. Surface Domain:

V. Surface Domain Datasets (Dsets):

a. Sample dataset output by ROI2dataset:

W. Surface State:

X. Volume Domain:

IV. Troubleshooting:

A. X server crash with 'w' option:

V. Figure List:

VI. Table of Contents