dipy_reslice#

Synopsis#

Reslice data to a new voxel resolution with automatic or manual sizing.

This workflow resamples volumetric data to a specified voxel size or automatically determines an optimal isotropic resolution. When automatic calculation is used, the new voxel size balances data quality with computational efficiency by interpolating between the original voxel dimensions.

Usage#

dipy_reslice [OPTIONS] input_files

Input Parameters#

  • input_files

    Path to the input volumes. This path may contain wildcards to process multiple inputs at once.

General Options#

  • --new_vox_size

    New voxel size as (x, y, z) in mm. If None, it will be automatically calculated using the formula: new_vox = voxel_sorted[1] + (voxel_sorted[2] - voxel_sorted[1]) * vox_factor where voxel_sorted are the original voxel dimensions sorted in ascending order. The calculated value is applied isotropically to all three dimensions. (default: None)

  • --order

    order of interpolation, from 0 to 5, for resampling/reslicing, 0 nearest interpolation, 1 trilinear etc.. if you don’t want any smoothing 0 is the option you need. (default: 1)

  • --mode

    Points outside the boundaries of the input are filled according to the given mode ‘constant’, ‘nearest’, ‘reflect’ or ‘wrap’. (default: constant)

  • --cval

    Fill value for points outside the input boundaries when mode=’constant’. (default: 0)

  • --num_processes

    Split the calculation to a pool of children processes. This only applies to 4D data arrays. Default is 1. If < 0 the maximal number of cores minus num_processes + 1 is used (enter -1 to use as many cores as possible). 0 raises an error. (default: 1)

  • --vox_factor

    Interpolation factor for automatic voxel size calculation, ranging from 0.0 to 1.0. Controls the trade-off between the second-largest and largest original voxel dimensions. 0.0: uses second-largest voxel size (finer resolution). 1.0: uses largest voxel size (coarser resolution). 0.14: recommended value for balanced resolution. Only used when new_vox_size is None. (default: 0.14)

Output Options#

  • --out_dir

    Output directory for saving results. (default: current directory)

  • --out_resliced

    Filename for the resliced output volume. (default: resliced.nii.gz)

References#

Garyfallidis, E., M. Brett, B. Amirbekian, A. Rokem, S. Van Der Walt, M. Descoteaux, and I. Nimmo-Smith. Dipy, a library for the analysis of diffusion MRI data. Frontiers in Neuroinformatics, 1-18, 2014.

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