sct_dmri_compute_dti

Compute Diffusion Tensor Images (DTI) using dipy.

usage: sct_dmri_compute_dti -i <file> -bval <file> -bvec <file>
                            [-method {standard,restore}] [-evecs {0,1}]
                            [-m <file>] [-o <str>] [-h] [-v <int>]
                            [-profile-time [<file>]] [-trace-memory [<folder>]]

MANDATORY ARGUMENTS

-i

Input 4d file. Example: dmri.nii.gz

-bval

Bvals file. Example: bvals.txt

-bvec

Bvecs file. Example: bvecs.txt

OPTIONAL ARGUMENTS

-method

Possible choices: standard, restore

Type of method to calculate the diffusion tensor:

  • standard: Standard equation [Basser, Biophys J 1994]

  • restore: Robust fitting with outlier detection [Chang, MRM 2005]

Default: “standard”

-evecs

Possible choices: 0, 1

Output tensor eigenvectors and eigenvalues.

Default: 0

-m

Mask used to compute DTI in for faster processing. Example: mask.nii.gz

-o

Output prefix.

Default: “dti_”

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/7.0/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/7.0/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.