NiftiProcessing

A nifti file processing tool

Under development

This software has NOT been approved for medical analysis/diagnosis. Please use other approved software in for medical use.

Options

positional arguments:
  path                  Path to file

optional arguments:
  -h, --help            show this help message and exit
  --precision {32,64}   Sets datatype precision in float32 or 64
  --info, -i            Outputs .nii file metadata
  --plot PLOT, -p PLOT  Plots image of 2nd/3rd dimension in .nii file 
                        (Requires MatplotLib)
  --align, -a           Orients .nii file in MNI152 space
  --normalize, -n       Normalizes .nii file values within set values 
                        (Default: 0.,1.)
  --normalize-lower     Lower value for normalization (Default: 0.)
  --normalize-upper     Lower value for normalization (Default: 0.)
  --rotate, -r          Rotates .nii file by 90 degress in 1st and 2nd dimension
  --output, -o          Filename for .nii file generation 
                        (Note: Currently erases orginal metadata)

Usage Examples

# Orients nifti file to MNI152 space
$ niftiprocessing sample.nii.gz -a -o output.nii.gz

# Plot slice 150 with matplotlib
$ niftiprocessing sample.nii.gz -p 150

Actions to implement:

Input

• Single
• Batch (directory)

Tools

• resize
• resize with pad
• resize with crop
• flip
• rotate
• invert
• denoise
• normalize
• align

Information

• scan information

Visualize

• terminal drawing output for orientation

Output

• Single
• Batch (directory)