Collection of ITK scripts for small stuff

General Information

Useful information about ITK

Dimensions {x, y. z} corresponds to [0], [1], [2] when workin with ITK arrays that uses those dimensions/directions (index, size etc.)

Read more about ITK at itk.org

Useful information about styles

• For input, type means the file type associated with filename.
• The scrips make output filenames themselves by using the input filename and append useful information about what happened.
• If the program runs with more arguments than specified, the program will EXIT_FAILURE.
• If the program runs with less arguments than specified, default arguments will be ran.
  

Scripts

HistogramSlice

Incomplete. From a 3D volume take out the middle slice (accordance to some direction), and use it to histogram match parallel slices

IntenseSlice

Complete. Take in two slices of images and compute some regional information based on 2D coordinate inputs.

Arguments: ./IntenseSlice [filename1] [filename2] [type] [x] [y] [step]

Default: ./IntenseSlice slice000 slice001 .tif 25 25 15

NormalizeIntense

Complete. Take a 2D slice and then normalize them by regional parameters.
Working on. Take a 3D volume, work on each slice like above.

Arguments: ./NormalizeIntese [filename] [type] [x] [y] [step]

Default: ./NormalizeIntense slice000 .tif 25 25 10

MaximumProjection

Complete. Take the maximum value of a direction to output a projection.

Arguments: ./MaximumProjection [filename] [type] [direction]

Default: ./MaximumProjection volume .nii.gz 0

ExtractSlice

Complete. extract a 2D slice depending on direction

Arguments: ./ExtractSlice [filename] [outType] [direction] [slice#]

Default: ./ExtractSlice proj_norm.nii .tif 0

More

Useful c3d commands

• c3d slice{000..499)_Norm.tif -tile z -o volume.nii.gz
• c3d Smallfield_OCT_Angiography_Volume_fovea.nii -slice x 0:-1 -oo slice%03d.tif
• c3d volume_250_250_200.nii.gz -stretch 0% 100% 0 255 volume_250_250_200_rescaled.nii.gz (This command has problems)

Useful ImageMath commands

• ImageMath volume_norm_tif.nii -rescale 0,255 -type float -outfile volume_imagemath.nii

Useful bash commands

• for i in {000..499}; do ./NormalizeIntense slice$i .nii 250 250 200; done

Author and Acknowledgements

Author: Viet Than, Department of EECS, Vanderbilt University, US.
Supervisor: Ipek Oguz, Prof. Department of EECS, Vanderbilt University, US.

With the help of the Medical Image Computing Lab.