sct_resample

Anisotropic resampling of 3D or 4D data.

usage: sct_resample -i <file> [-f <str>] [-mm <str>] [-vox <str>] [-ref <file>]
                    [-x {nn,linear,spline}] [-o <file>] [-h] [-v <int>]
                    [-profile-time [<file>]] [-trace-memory [<folder>]]

MANDATORY ARGUMENTS

-i

Image to resample. Can be 3D or 4D. (Cannot be 2D) Example: dwi.nii.gz

METHOD TO SPECIFY NEW SIZE: Please choose only one of the 4 options

-f

Resampling factor in each dimensions (x,y,z). Separate with x. Example: 0.5x0.5x1

For 2x upsampling, set to 2. For 2x downsampling set to 0.5

-mm

New resolution in mm. Separate dimension with x. Example: 0.1x0.1x5

Note: Resampling can only approximate a desired mm resolution, given the limitations of discrete voxel data arrays.

-vox

Resampling size in number of voxels in each dimensions (x,y,z). Separate with x.

-ref

Reference image to resample input image to. The voxel dimensions and affine of the reference image will be used.

OPTIONAL ARGUMENTS

-x

Possible choices: nn, linear, spline

Interpolation method.

Default: “linear”

-o

Output file name. Example: dwi_resampled.nii.gz

MISC ARGUMENTS

-v

Possible choices: 0, 1, 2

Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode.

Default: 1

-profile-time

Enables time-based profiling of the program, dumping the results to the specified file.

If no file is specified, human-readable results are placed into a ‘time_profiling_results.txt’ document in the current directory (’/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/stable/documentation/source’). If the specified file is a .prof file, the file will instead be in binary format, ready for use with common post-profiler utilities (such as snakeviz).

-trace-memory

Enables memory tracing of the program.

When active, a measure of the peak memory (in KiB) will be output to the file peak_memory.txt. Optionally, developers can also modify the SCT code to add additional snapshot_memory() calls. These calls will ‘snapshot’ the memory usage at that moment, saving the memory trace at that point into a second file (memory_snapshots.txt).

By default, both outputs will be placed in the current directory (’/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/stable/documentation/source’). Optionally, you may provide an alternative directory (-trace-memory <dir_name>), in which case all files will be placed in that directory instead. Note that this WILL incur an overhead to runtime, so it is generally advised that you do not run this in conjunction with the time profiler or in time-sensitive contexts.