StereotaxicRAMON

General commands

commands

List all commands

help(name)

Print help on command a command

penSize(size_in_pixels)

Arg[1]=size in pixels

setMouse(mouse_mode)

Change mouse mode to arg[1]={sample,paint,select,cselect,poly,fill}

Commands acting the volume data

abs

Absolute value

addConstant(value)

Add 'value' (a float number) to the volume values

multiplyConstant(value)

Multiply the volume values by arg[1]

applyRotation

Apply current rotation

boxFilter(filter_size,iterations)

Arg[1]=filter size, arg[2]=iterations

changePixdim(dim_x,dim_y,dim_z)

Change voxel dimensions in the header

convertToMovie(path)

Convert slices into mp4 movie stored at path arg[1]

crop

Crops volume to the bounding box of the selection

mode

Change value of each voxel in the selection by the mode of a neighbourhood of size 7x7x7

polygonize(path)

Save a mesh of the selection at arg[1]=path

reorient(new_orientation)

Change the current 'xyz' orientation of the volume to that of the string in arg[1], for example, zxy

resample(x_dim,y_dim,z_dim,interpolation)

Resample volume to pixel dimensions arg[1-3], using arg[4]={nearest,trilinear} interpolation

resize(x_dim,y_dim,z_dim,justification)

Resize volume to dimension arg[1-3], arg[4]=three characters containing the justification flags s=start, c=center, e=end for the x, y and z dimensions (for example ssc=x start, y start, z center)

save

Overwrite volume

saveAs(path)

Save data volume at arg[1]=path

savePicture(path)

Save current image at arg[1]=path

set(value)

Set the selected voxels to 'value'

setRotation(x_rotation,y_rotation,z_rotation)

Rotate the volume arg[1-3]=angle x, y, z, in degrees

setVolume(path)

Reload volume

stdev(neighbourhood,maximum)

Replaces volume by the local standard deviation of its values, clipping the maximum

Mathematical morphology operators

dilate(size_in_voxels)

Dilate selection arg[1]=number of voxels

erode(size_in_voxels)

Erode selection arg[1]=number of voxels

tpDilate(size_in_voxels)

Topology-preserving dilate selection arg[1]=number of voxels

tpDilateOnMask(size_in_voxels,path_to_mask)

Topology-preserving dilate selection inside a mask, arg[1]=number of voxels, arg[2]=path a mask with the same dimensions as the current volume

tpErode(size_in_voxels)

Topology-preserving erode selection arg[1]=number of voxels

3D Fourier transform

dct

Direct cosine transform

idct

Inverse discrete cosine transform

Measure

minMax

Print minimum and maximum values

histogram

Histogram of volume's selected values

info

Display file header information

stats

Prints summary statistics of the selection

Commands acting on the selection

addSelection(path)

Add selection from arg[1]=path

loadSelection(path)

Load selection at arg[1]=path

saveSelection(path)

Save selection at arg[1]=path

subtractSelection(path)

Subtract selection from arg[1]=path

boundingBox

Select the smallest box including all currently selected voxels

box(xmin,ymin,zmin,xmax,ymax,zmax)

Select the region inside the box arg[1-6]=xmn,ymn,zmn,xmx,ymx,zmx

connectedSelection(x,y,z)

Keeps only the selection connected to coordinate x,y,z

deselect

Clears the selection

euler

Display Euler's characteristic for the selection

fill(x,y,z,plane)

Fills in 2D starting at coordinates arg[1-3]=x,y,z in plane arg[4]=X, Y or Z

grow(min,max)

Add to the actual selection connected voxels with values between arg[1,2]=min,max

make26

Remove edge and corner neighbours so as to make the selection 26 connected

invert

Invert selection

select(x_coord,y_coord,z_coord,min_value,max_value)

Select voxels around x_coord,y_coord,z_coord with values within min_value and max_value

setThresholdWidth(width)

Expand the threshold to include values within the width

smooth(threshold,n_iterations)

Smooth selection by removing all voxels with less than threshold, for n_iterations

threshold(value,direction)

Select values from arg[1]=threshold and down if arg[2]=0 or up if arg[2]=1

undo

Undoes as much as possible of the previous action

Display

adjustMinMax

Adjust min and max grey level values to mean ± 2 standard deviations (clipped to the volume's min and max)

colormap(name)

Colormap name is a string among {autumn, bone, winter, hot, water, solidred, solidrgb, jet, jetrgb, negpos, gray}

setMinMax(min,max)

Change the min,max values used for display to arg[1,2]=min,max

setSelectionColor(red,green,blue)

Change selection color to RGB=arg[1-3]

setSelectionOpacity(opacity)

Change selection opacity to arg[1]

Mesh commands

flipMesh(plane)

Flips the mesh (if loaded) along the dimension argv[1]=x, y or z

loadMesh(path)

Load a mesh in text format at arg[1]=path

pushMesh(distance)

Push the mesh (if loaded) by arg[1]=distance along the normal

reorientMesh(new_orientation)

Change the current 'xyz' orientation of the mesh (if loaded) to that of the string in arg[1], for example, zxy

saveMesh(path)

Save mesh (if loaded) at arg[1]=path

scaleMesh(value)

Scale mesh (if loaded) with arg[1]=scale factor

translateMesh(x,y,z)

Translate mesh (if loaded) by adding arg[1-3]=x, y and z displacements

voxeliseMesh

Voxelise mesh (if loaded)