Command Line Interface

DECAES provides a command line interface (CLI) for calling the main analysis functions: T2mapSEcorr for computing $T_2$-distributions, and T2partSEcorr for running $T_2$-parts analysis on the resulting $T_2$-distributions for computing measures such as the myelin water fraction.

Using the CLI

Assuming you have DECAES installed, there are two equivalent ways to use the CLI:

1. Helper script: Create a simple Julia script which calls the entrypoint function main provided by this package. For example, save the following code in a Julia script called decaes.jl:

using DECAES # load the package
main() # call command line interface

An image file image.nii can be passed to DECAES by running this script with julia from the command line:

$ julia decaes.jl image.nii <COMMAND LINE ARGS>

2. Julia -e flag: The contents of the above script can equivalently be passed directly to julia using the -e (for "evaluate") flag:

$ julia -e 'using DECAES; main()' -- image.nii <COMMAND LINE ARGS>

Either way of calling the CLI forwards the arguments <COMMAND LINE ARGS> to the entrypoint function main. Available command line arguments are detailed in the Arguments section.

For the remainder of this section, we will make use of the decaes.jl script from option 1.

File types

Input files must be one of the following file types:

  1. NIfTI file with extension .nii, or gzip compressed NIfTI file with extension .nii.gz. See NIfTI.jl for more information.
  2. MATLAB file with extension .mat. Note:.mat files saved in the oldest format v4 are not supported, but all newer formats (v6, v7, and v7.3) are supported. See MAT.jl for more information.
  3. Philips PAR/REC file pair with extensions .par and .rec (or .PAR and .REC).
  4. Philips XML/REC file pair with extensions .xml and .rec (or .XML and .REC).

All output files are saved as .mat files in format v7.3.

Note

If your data is in DICOM format, the freely available dcm2niix tool is able to convert DICOM files into NIfTI format

Note
  • Input files are interpreted as 4D arrays (or 3D arrays for mask files) when loaded; ensure that the underlying data is stored with the first three dimensions as (row, column, slice), and the last dimension as echo (or $T_2$ bin, or omitted for mask files)
  • Images read from NIfTI and PAR/XML/REC files are coerced into the appropriate dimension; errors or unexpected behaviour may occur if the data is not stored with the correct dimensions
  • MATLAB files are searched for arrays with the appropriate dimension; the first such array that is found is used, otherwise an error will occur. Multiple 3D/4D arrays should not be stored in the same .mat file)

Arguments

Available command line arguments are broken into four categories:

  1. Positional arguments: these are the input files. Input files are typically placed at the beginning of <COMMAND LINE ARGS>.
  2. Optional arguments: settings governing the analysis pipeline. See below for details.
  3. T2mapSEcorr/T2partSEcorr arguments: settings for computing the $T_2$-distribution and subsequent $T_2$-parts analysis. See below for the full parameter list; see T2mapSEcorr and T2partSEcorr for parameter descriptions. Note: if no default is shown, the parameter is unused by default.
  4. BET arguments: settings for governing automatic brain mask generation using the BET brain extraction tool; see below for details.
usage: <PROGRAM> [--mask MASK [MASK...]] [-o OUTPUT] [--T2map]
                 [--T2part] [--quiet] [--dry] [--legacy]
                 [--Chi2Factor CHI2FACTOR] [--MinRefAngle MINREFANGLE]
                 [--MPWin MPWIN MPWIN] [--nRefAngles NREFANGLES]
                 [--nRefAnglesMin NREFANGLESMIN] [--nT2 NT2]
                 [--RefConAngle REFCONANGLE] [--Reg REG]
                 [--SaveDecayCurve] [--SaveNNLSBasis] [--SaveRegParam]
                 [--SaveResidualNorm] [--SetFlipAngle SETFLIPANGLE]
                 [--Sigmoid SIGMOID] [--Silent] [--SPWin SPWIN SPWIN]
                 [--T1 T1] [--T2Range T2RANGE T2RANGE] [--TE TE]
                 [--Threshold THRESHOLD] [--bet] [--betargs BETARGS]
                 [--betpath BETPATH] input...

positional arguments:
  input                 one or more input filenames. Valid file types
                        are limited to: .mat, .nii, .nii.gz, .par,
                        .xml, and .rec

optional arguments:
  --mask MASK [MASK...]
                        one or more mask filenames. Masks are loaded
                        and subsequently applied to the corresponding
                        input files via elementwise multiplication.
                        The number of mask files must equal the number
                        of input files. Valid file types are the same
                        as for input files, and are limited to: .mat,
                        .nii, .nii.gz, .par, .xml, and .rec
  -o, --output OUTPUT   output directory. If not specified, output
                        file(s) will be stored in the same location as
                        the corresponding input file(s). Outputs are
                        stored with the same basename as inputs and
                        additional suffixes; see --T2map and --T2part
  --T2map               call T2mapSEcorr to compute T2 distributions
                        from 4D multi spin-echo input images. T2
                        distributions and T2 maps produced by
                        T2mapSEcorr are saved as MAT files with
                        extensions .t2dist.mat and .t2maps.mat
  --T2part              call T2partSEcorr to analyze 4D T2
                        distributions to produce parameter maps. If
                        --T2map is also passed, input 4D arrays are
                        interpreted as multi spin-echo images and T2
                        distributions are first computed by
                        T2mapSEcorr. If only --T2part is passed, input
                        4D arrays are interpreted as T2 distributions
                        and only T2partSEcorr is called. Output T2
                        parts are saved as a MAT file with extension
                        .t2parts.mat
  --quiet               suppress printing to the terminal. Note: 1)
                        errors are not silenced, and 2) this flag
                        overrides the --Silent flag in T2mapSEcorr
  --dry                 execute dry run of processing without saving
                        any results
  --legacy              use legacy settings and algorithms from the
                        original MATLAB version. This ensures that the
                        exact same T2-distributions and T2-parts will
                        be produced as those from MATLAB (to machine
                        precision). Note that execution time will be
                        much slower.

T2mapSEcorr/T2partSEcorr arguments:
  --Chi2Factor CHI2FACTOR
                        (default: 1.02)
  --MinRefAngle MINREFANGLE
                        (default: 50.0)
  --MPWin MPWIN MPWIN    (default: [0.025, 0.2])
  --nRefAngles NREFANGLES
                        (default: 32)
  --nRefAnglesMin NREFANGLESMIN
                        (default: 5)
  --nT2 NT2              (default: 40)
  --RefConAngle REFCONANGLE
                        (default: 180.0)
  --Reg REG              (default: "chi2")
  --SaveDecayCurve
  --SaveNNLSBasis
  --SaveRegParam
  --SaveResidualNorm
  --SetFlipAngle SETFLIPANGLE

  --Sigmoid SIGMOID
  --Silent
  --SPWin SPWIN SPWIN    (default: [0.01, 0.025])
  --T1 T1                (default: 1.0)
  --T2Range T2RANGE T2RANGE
                        (default: [0.01, 2.0])
  --TE TE                (default: 0.01)
  --Threshold THRESHOLD
                        (default: 200.0)

BET arguments:
  --bet                 use the BET brain extraction tool from the FSL
                        library of analyis tools to automatically
                        create a binary brain mask. Only voxels within
                        the binary mask will be analyzed. Note that if
                        a mask is passed explicitly with the --mask
                        flag, this mask will be used and --bet will be
                        ignored.
  --betargs BETARGS     BET optional arguments. Must be passed as a
                        single string with arguments separated by
                        spaces, e.g. '-m -n'. The flag '-m' creates
                        the binary mask and will be added to the list
                        of arguments if not provided. (default: "-m -n
                        -f 0.25 -R")
  --betpath BETPATH     path to BET executable. (default: "bet")
Note

If desired, the $T_2$-distribution computation and the $T_2$-parts analysis may be performed separately:

  • When the --T2map flag is passed, or both --T2map and --T2part flags are passed, input image arrays should be 4D with data as (row, column, slice, echo)
  • When only the --T2part flag is passed, input image arrays should be 4D with data as (row, column, slice, $T_2$ bin)

Outputs

DECAES will produce up to five output files, each with the input filename (without suffix) used as a prefix. For example, if the input file is called image.nii, the possible output files are:

  1. image.t2dist.mat: MATLAB file containing the 4D array of $T_2$-distributions (produced when --T2map flag is passed)
  2. image.t2maps.mat: MATLAB file containing $T_2$-distribution property maps and NNLS fit parameters; see T2mapSEcorr (produced when --T2map flag is passed)
  3. image.t2parts.mat: MATLAB file containing $T_2$-parts analysis results such as the MWF; see T2partSEcorr (produced when --T2part flag is passed)
  4. image.log: Log file containing the console output
  5. image.settings.txt: Copy of settings file which was named settings.txt (produced when passing settings as a file)

If the --dry flag is passed, none of the above files will be produced.

Multithreading

Multithreaded parallel processing can be enabled by setting the JULIA_NUM_THREADS environment variable as follows:

$ export JULIA_NUM_THREADS=1 # set JULIA_NUM_THREADS > 1 to enable parallel processing
$ julia decaes.jl image.nii <COMMAND LINE ARGS>

This is highly recommended to speed up computation time, but is not strictly required.

Note

From the Julia documentation:

[The keyword export] works on bourne shells on Linux and OSX. Note that if you're using a C shell on these platforms, you should use the keyword set instead of export. If you're on Windows, start up the command line in the location of julia.exe and use set instead of export.

Examples

Default options

Suppose you have a multi spin-echo image file image.nii which you would like to perform $T_2$ analysis on. We can call T2mapSEcorr and T2partSEcorr on the file image.nii with default options using decaes.jl as follows:

$ export JULIA_NUM_THREADS=1
$ julia decaes.jl image.nii --T2map --T2part

After a few seconds, the script should begin running with the following messages appearing as the script progresses (note that real images will take longer to process than this toy example):

[ Info: Starting with 1 threads

[ Info: Loading input file: image.nii.gz ...
[ Info: Done (0.17 seconds)

[ Info: Running T2mapSEcorr on file: image.nii.gz ...
┌ Info: T2-Distribution analysis settings:
│     Chi2Factor       : 1.02
│     legacy           : false
│     MatrixSize       : (100, 100, 1)
│     MinRefAngle      : 50.0
│     nRefAngles       : 32
│     nRefAnglesMin    : 5
│     nT2              : 40
│     nTE              : 32
│     RefConAngle      : 180.0
│     Reg              : chi2
│     SaveDecayCurve   : false
│     SaveNNLSBasis    : false
│     SaveRegParam     : false
│     SaveResidualNorm : false
│     SetFlipAngle     : nothing
│     Silent           : false
│     T1               : 1.0
│     T2Range          : (0.01, 2.0)
│     TE               : 0.01
└     Threshold        : 200.0
[ Info: [  0%] -- Elapsed Time: 00h:00m:00s -- Estimated Time Remaining: --h:--m:--s
[ Info: [ 25%] -- Elapsed Time: 00h:00m:15s -- Estimated Time Remaining: 00h:00m:43s
[ Info: [ 51%] -- Elapsed Time: 00h:00m:30s -- Estimated Time Remaining: 00h:00m:28s
[ Info: [ 77%] -- Elapsed Time: 00h:00m:45s -- Estimated Time Remaining: 00h:00m:13s
[ Info: [100%] -- Elapsed Time: 00h:00m:57s -- Estimated Time Remaining: 00h:00m:00s
[ Info: Done (58.12 seconds)

[ Info: Saving T2 distribution to file: image.t2dist.mat ...
[ Info: Done (0.32 seconds)

[ Info: Saving T2 parameter maps to file: image.t2maps.mat ...
[ Info: Done (0.11 seconds)

[ Info: Running T2partSEcorr ...
┌ Info: T2-part analysis settings:
│     legacy     : false
│     MatrixSize : (100, 100, 1)
│     MPWin      : (0.025, 0.2)
│     nT2        : 40
│     Sigmoid    : nothing
│     Silent     : false
│     SPWin      : (0.01, 0.025)
└     T2Range    : (0.01, 2.0)
[ Info: Done (0.09 seconds)

[ Info: Saving T2 parts maps to file: image.t2parts.mat ...
[ Info: Done (0.0 seconds)

[ Info: Finished (58.85 seconds)

Multiple input files

Multiple input files (possibly of different file types) can be passed in the obvious way:

$ export JULIA_NUM_THREADS=1
$ julia decaes.jl image1.nii image2.mat image3.nii.gz image4.par --T2map --T2part

Specify output folder

By default, output files are saved in the same location as the corresponding input file. If you'd like to save them in a different folder, you can use the -o or --output flag:

$ export JULIA_NUM_THREADS=1
$ julia decaes.jl image.nii --T2map --T2part --output /path/to/output/folder/

The requested output folder will be created if it does not already exist.

Non-default parameters

Parameter values can be set to non-default values at the command line. For example, we can set the echo time TE to 8ms, the number of $T_2$ bins nT2 to 60, and the $T_2$ distribution range to [10ms, 1.5s] as follows:

$ export JULIA_NUM_THREADS=1
$ julia decaes.jl image.nii --T2map --T2part --TE 0.008 --nT2 60 --T2Range 0.010 1.5

Passing image masks

Image masks can be passed into DECAES using the --mask flag:

$ export JULIA_NUM_THREADS=1
$ julia decaes.jl image.nii --T2map --T2part --mask mask.nii

The mask file is loaded and applied to the input image via elementwise multiplication over the spatial dimensions, e.g. the mask is applied to each echo of a 4D multi-echo input image.

If multiple image files are passed, a mask can be passed for each input image (note that each mask file can be any valid file type):

$ export JULIA_NUM_THREADS=1
$ julia decaes.jl image1.nii image2.mat --T2map --T2part --mask mask1.mat mask2.nii.gz
Note

If input images have been manually masked such that they are zero outside regions of interest, a mask need not be passed. The --Threshold parameter of T2mapSEcorr controls a first echo intensity cutoff threshold (default value 200.0), below which voxels are automatically skipped during processing

Automatic brain masking with BET

The BET brain extraction tool from the FSL library of analysis tools can be used to automatically generate a brain mask prior to analysis. Only voxels within the generated brain mask will be processed, greatly reducing analysis time. To use BET, pass the --bet flag:

$ export JULIA_NUM_THREADS=1
$ julia decaes.jl image.nii --T2map --T2part --bet

If bet is not on your system path, you can pass the path to the bet binary with the --betpath flag. Additionally, you can pass arguments to bet with the --betargs flag:

$ export JULIA_NUM_THREADS=1
$ julia decaes.jl image.nii --T2map --T2part --bet --betpath /path/to/bet --betargs '-m -n'

Note that bet arguments must be passed as a single string to --betargs, separated by spaces, as shown above.

Note

If a mask file is passed using the --mask flag, the --bet flag will be ignored and the mask file will be used

Settings files

Parameter values can be read in from a settings file. For example, we can combine the examples from the Specify output folder and Non-default parameters sections by creating a settings.txt file with the following contents:

/path/to/image.nii
--output
/path/to/output/folder/
--T2map
--T2part
--TE
0.008
--nT2
60
--T2Range
0.010
1.5

If this file is located at /path/to/settings.txt, simply prefix the filepath with the @ character to have the file contents read into the main function:

$ export JULIA_NUM_THREADS=1
$ julia decaes.jl @/path/to/settings.txt
Note
  • The use of settings files is highly recommended for both reproducibility and for self-documentation. The input settings file will be automatically copied into the output folder for each processed image, with the image filename prepended. In this case, for example, the copied settings file would be called image.settings.txt
  • Only one flag or value is allowed per line within a settings file. Flags which require multiple inputs (e.g. --T2Range above) must use one line for each input
  • The extension of the settings file is ignored; .txt is arbitrary in this example
  • Though not strictly necessary, using full input- and output paths is recommended. This way, one doesn't rely on relative paths and can e.g. call julia /path/to/decaes.jl @/path/to/settings.txt from any directory

Legacy options

During the MATLAB port to Julia, some algorithms were improved using computationally more efficient algorithms, and some default parameters were modified as well. This may cause small differences in output parameter maps. As an example, the flip angle optimization procedure requires finding the root of a cubic spline. In MATLAB this was performed by evaluating the spline on a very fine mesh and choosing the value nearest zero. During profiling it was found that this was a time consuming operation, and therefore in Julia this was replaced by an efficient rootfinding method tailored for cubic splines.

The differences due to algorithmic changes like the one above are quite small. For example, most tests in the DECAES test suite will pass when using a relative tolerance of $10^{-3}$, and almost all tests pass with a relative tolerance of $10^{-2}$. That is to say that nearly all outputs are identical to 3 or more significant digits, which includes $T_2$-distributions, MWF maps, etc. It should be emphasized, though, that as these differences arise from improved algorithms, any discrepencies are merely small improvements.

The --legacy flag is available if exact reproducibility is required compared to the MATLAB version. This will ensure that all outputs match to nearly machine precision (a relative tolerance of $10^{-10}$ is used during testing). Note however that the --legacy flag may cause a significant slowdown in processing time due to less efficient algorithms being used internally, and is therefore not recommended unless absolutely necessary. Differences due to changes in default parameters can always be overridden by passing in the desired value explicitly (e.g. --SPWin 0.014 0.040) without the need for the --legacy flag.

Default options with the --legacy flag

usage: <PROGRAM> [--mask MASK [MASK...]] [-o OUTPUT] [--T2map]
                 [--T2part] [--quiet] [--dry] [--legacy]
                 [--Chi2Factor CHI2FACTOR] [--MinRefAngle MINREFANGLE]
                 [--MPWin MPWIN MPWIN] [--nRefAngles NREFANGLES]
                 [--nRefAnglesMin NREFANGLESMIN] [--nT2 NT2]
                 [--RefConAngle REFCONANGLE] [--Reg REG]
                 [--SaveDecayCurve] [--SaveNNLSBasis] [--SaveRegParam]
                 [--SaveResidualNorm] [--SetFlipAngle SETFLIPANGLE]
                 [--Sigmoid SIGMOID] [--Silent] [--SPWin SPWIN SPWIN]
                 [--T1 T1] [--T2Range T2RANGE T2RANGE] [--TE TE]
                 [--Threshold THRESHOLD] [--bet] [--betargs BETARGS]
                 [--betpath BETPATH] input...

positional arguments:
  input                 one or more input filenames. Valid file types
                        are limited to: .mat, .nii, .nii.gz, .par,
                        .xml, and .rec

optional arguments:
  --mask MASK [MASK...]
                        one or more mask filenames. Masks are loaded
                        and subsequently applied to the corresponding
                        input files via elementwise multiplication.
                        The number of mask files must equal the number
                        of input files. Valid file types are the same
                        as for input files, and are limited to: .mat,
                        .nii, .nii.gz, .par, .xml, and .rec
  -o, --output OUTPUT   output directory. If not specified, output
                        file(s) will be stored in the same location as
                        the corresponding input file(s). Outputs are
                        stored with the same basename as inputs and
                        additional suffixes; see --T2map and --T2part
  --T2map               call T2mapSEcorr to compute T2 distributions
                        from 4D multi spin-echo input images. T2
                        distributions and T2 maps produced by
                        T2mapSEcorr are saved as MAT files with
                        extensions .t2dist.mat and .t2maps.mat
  --T2part              call T2partSEcorr to analyze 4D T2
                        distributions to produce parameter maps. If
                        --T2map is also passed, input 4D arrays are
                        interpreted as multi spin-echo images and T2
                        distributions are first computed by
                        T2mapSEcorr. If only --T2part is passed, input
                        4D arrays are interpreted as T2 distributions
                        and only T2partSEcorr is called. Output T2
                        parts are saved as a MAT file with extension
                        .t2parts.mat
  --quiet               suppress printing to the terminal. Note: 1)
                        errors are not silenced, and 2) this flag
                        overrides the --Silent flag in T2mapSEcorr
  --dry                 execute dry run of processing without saving
                        any results
  --legacy              use legacy settings and algorithms from the
                        original MATLAB version. This ensures that the
                        exact same T2-distributions and T2-parts will
                        be produced as those from MATLAB (to machine
                        precision). Note that execution time will be
                        much slower.

T2mapSEcorr/T2partSEcorr arguments:
  --Chi2Factor CHI2FACTOR
                        (default: 1.02)
  --MinRefAngle MINREFANGLE
                        (default: 50.0)
  --MPWin MPWIN MPWIN    (default: [0.04, 0.2])
  --nRefAngles NREFANGLES
                        (default: 8)
  --nRefAnglesMin NREFANGLESMIN
                        (default: 8)
  --nT2 NT2              (default: 40)
  --RefConAngle REFCONANGLE
                        (default: 180.0)
  --Reg REG              (default: "chi2")
  --SaveDecayCurve
  --SaveNNLSBasis
  --SaveRegParam
  --SaveResidualNorm
  --SetFlipAngle SETFLIPANGLE

  --Sigmoid SIGMOID
  --Silent
  --SPWin SPWIN SPWIN    (default: [0.014, 0.04])
  --T1 T1                (default: 1.0)
  --T2Range T2RANGE T2RANGE
                        (default: [0.015, 2.0])
  --TE TE                (default: 0.01)
  --Threshold THRESHOLD
                        (default: 200.0)

BET arguments:
  --bet                 use the BET brain extraction tool from the FSL
                        library of analyis tools to automatically
                        create a binary brain mask. Only voxels within
                        the binary mask will be analyzed. Note that if
                        a mask is passed explicitly with the --mask
                        flag, this mask will be used and --bet will be
                        ignored.
  --betargs BETARGS     BET optional arguments. Must be passed as a
                        single string with arguments separated by
                        spaces, e.g. '-m -n'. The flag '-m' creates
                        the binary mask and will be added to the list
                        of arguments if not provided. (default: "-m -n
                        -f 0.25 -R")
  --betpath BETPATH     path to BET executable. (default: "bet")