manualreslice

• purpose
• usage
• examples
• comments
• error messages
• see also

Purpose:

This is the only interactive program in the AIR package and it serves four roles. Given values for rigid body transformation parameters (x_shift,y_shift, z_shift,roll, pitch and yaw) with or without 3 scaling parameters, it can:

1. Convert these values into an initialization file for use with an AIR alignment program (example 1).
2. Use these values to reslice a file to generate a new file with specified voxel dimensions and matrix size (example 2)
3. Create a .air file based on these values that can be used by other programs such as reslice, combine_air, combine_warp and invert_air (example 2).
4. Generate a .air file that will interpolate a specified image file to cubic voxels based on the same top alignment assumptions utilized by the programs zoomer and reslice (example 3).

Usage:

manualreslice

NOTE:

Supply information and answer the questions at the prompts

Shifts are defined in units of cubified reslice file voxels. In other words, if the file that you are planning to reslice has anisotropic voxel sizes, you must envision the file as having been interpolated to cubic voxels when specifying shifts. For example, if your voxels are anisotropic with a larger z size than x and y size, a z-axis shift of 1 will shift you a distance equivalent to the x and y axis pixel size, not by 1 plane as you might otherwise expect).

Examples:

Example 1:

manualreslice

x-axis shift in voxels:0

y-axis shift in voxels:0

z-axis shift in voxels:0

roll (rotation around y-axis in degrees:0

pitch (rotation around x-axis in degrees:10

yaw (rotation around z-axis in degrees:0

x scale-down factor:1

y scale-down factor:1

z scale-down factor:1

Save parameters as initialization file for automated registration? (y/n):y

Name of initialization file to save:myfile.init

Parameters saved to initialization file myfile.init

Exit?(y/n):y

• This usage will save an initialization file called myfile.init specifying initialization with 10 degrees of pitch

Example 2:

manualreslice

x-axis shift in voxels:0

y-axis shift in voxels:0

z-axis shift in voxels:0

roll (rotation around y-axis in degrees:0

pitch (rotation around x-axis in degrees:10

yaw (rotation around z-axis in degrees:0

x scale-down factor:1

y scale-down factor:1

z scale-down factor:1

Save parameters as initialization file for automated registration? (y/n):n

[path/]name of file to reslice (no spaces allowed):pet1.img

Define target space by {e}xample file or {m}anually? (e/m):e

[path/]name of example file (no spaces allowed):pet2.img

Save a .air file based on the information provided? (y/n):y

Full name of .air file:pet1.airpet2

.air file saved as pet1.airpet2

Exit? (will proceed to reslice file if answer is no) (y/n):n

Output voxel dimensions will be 2 x 2 x 6

Would you prefer cubic voxels (2 x 2 x 2)? (y/n):n

[path/]name of output file (no spaces allowed):newpet1

Resliced file newpet1.img has been saved

• This usage will create a .air file that can be used in the future with the program reslice to reslice file pet1 with 10 degrees of pitch. Reslicing based upon the .air file pet1.airpet2 will generate a file that has the same matrix and voxel dimensions as file pet2.
• The matrix and voxel dimensions could have been specified manually by responding with 'm' instead of 'e' to the prompt about the target space.
• Because of the negative response to the last exit query, file pet1 was resliced to generate file newpet1 which has the same dimensions and matrix size as pet2. 10 degrees of pitch was applied in the course of reslicing.
• The option of interpolating file newpet1 to cubic voxels was offered but declined.

Example 3:

manualreslice

x-axis shift in voxels:0

y-axis shift in voxels:0

z-axis shift in voxels:0

roll (rotation around y-axis in degrees:0

pitch (rotation around x-axis in degrees:10

yaw (rotation around z-axis in degrees:0

x scale-down factor:1

y scale-down factor:1

z scale-down factor:1

Save parameters as initialization file for automated registration? (y/n):n

[path/]name of file to reslice (no spaces allowed):pet1

Define target space by {e}xample file or {m}anually? (e/m):m

The file you want to reslice has voxels with

x-dimension size of 1.745000e+00

y-dimension size of 1.745000e+00

z-dimension size of 6.750000e+00

What sizes do you want for voxels after reslicing?

x-dimension size:1.745

y-dimension size:1.745

z_dimension size:1.745

The file you want to reslice has matrix dimensions of

x-dimension 128

y-dimension 128

z-dimension 15

What dimensions do you want for matrix after reslicing?

x_dimension:128

y_dimension:128

z_dimension:55

Save a .air file based on the information provided? (y/n):y

Full name of .air file:pet1.airinterpolate

The two spaces that you have defined meet criteria suggesting that you may view them as identical except for interpolation error.

Do you want to treat them as spatially identical? (y/n):y

Parameters adjusted from center-center alignment to first_plane-first_plane alignment

Reslicing will reflect spatial identity

.air file saved as pet1.airinterpolate

Exit? (will proceed to reslice file if answer is no) (y/n):y

• This usage illustrates a special case handler in the program that allows you to create a .air file that will mimic the interpolation behavior of zoomer. By indicating that the files are spatially identical, the .air file that is created will reflect top-to-top alignment rather than center-to-center alignment that is otherwise the default for manualreslice.
• The option to treat files as spatially identical is only offered when the values of pitch, roll, yaw, x-shift, y-shift, and z-shift are all zero and all scale_down factors are 1. In addition, the dimensions of the target space must be equal to the interpolated dimensions of the reslice space based upon the top-to-top interpolation model, and the smallest voxel size in each of the two files must be identical.
• The -f option in zoomer provides a much easier way to generate the same .air file that this program will generate here.

Comments:

• Initialization files can be viewed and modified with a text editor. Do not be alarmed that the values are different from those that you typed in--the units and the order in which parameters are listed have been changed to meet the requirements of an initialization file. If the scale-down factors that you provide are all equal to 1, the program assumes that you want to generate a six parameter rigid body initialization file. If any of the scale-down factors is not exactly 1, a 3D nine parameter model initialization is provided.
• Rotations are defined to take place around the exact center of the files.
• Translations are defined in units of cubified reslice file voxels, so if your reslice file has anisotropic voxel sizes, you should envision the file as being interpolated to cubic voxels when specifying shifts.
• The order in which you enter the various parameters is conceptually the order in which the parameters are applied to the reslice file to resample it into the standard file space. This should make it possible to maintain a mental image of what the program is doing. Note that translations take place in the reslice file space, not in the final image (standard file) space. Rescaling takes place in the final image space. Note that when the AIR package actually performs reslicing, it must find the data in the reslice file that corresponds to each voxel in the output file, so the order in which shifts, rotations and rescalings are actually applied by the resamplng program must be reversed from the conceptual order used here.
• The ability to create a .air file manually will allow you to resample data to any voxel size and matrix dimensions that you like. By using combine_air you can combine the resizing with any other registration that needs to be performed to minimize reinterpolation of your data.

Error messages: (alphabetical)

See also: Generic error messages

Other error messages generated by this program are self explanatory

See also:

• reslice