【MRtrix】MRtrixを用いた拡散MRIの前処理 ～歪み・頭の動き・渦電流の補正～

SYNOPSIS

     Perform diffusion image pre-processing using FSL's eddy tool; including
     inhomogeneity distortion correction using FSL's topup tool if possible

USAGE

     dwifslpreproc [ options ] input output

        input        The input DWI series to be corrected

        output       The output corrected image series

DESCRIPTION

     This script is intended to provide convenience of use of the FSL software
     tools topup and eddy for performing DWI pre-processing, by encapsulating
     some of the surrounding image data and metadata processing steps. It is
     intended to simply these processing steps for most commonly-used DWI
     acquisition strategies, whilst also providing support for some more exotic
     acquisitions. The "example usage" section demonstrates the ways in which
     the script can be used based on the (compulsory) -rpe_* command-line
     options.

     The "-topup_options" and "-eddy_options" command-line options allow the
     user to pass desired command-line options directly to the FSL commands
     topup and eddy. The available options for those commands may vary between
     versions of FSL; users can interrogate such by querying the help pages of
     the installed software, and/or the FSL online documentation: (topup)
     https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide ; (eddy)
     https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide

     The script will attempt to run the CUDA version of eddy; if this does not
     succeed for any reason, or is not present on the system, the CPU version
     will be attempted instead. By default, the CUDA eddy binary found that
     indicates compilation against the most recent version of CUDA will be
     attempted; this can be over-ridden by providing a soft-link "eddy_cuda"
     within your path that links to the binary you wish to be executed.

     Note that this script does not perform any explicit registration between
     images provided to topup via the -se_epi option, and the DWI volumes
     provided to eddy. In some instances (motion between acquisitions) this can
     result in erroneous application of the inhomogeneity field during
     distortion correction. Use of the -align_seepi option is advocated in this
     scenario, which ensures that the first volume in the series provided to
     eddy is also the first volume in the series provided to eddy, guaranteeing
     alignment. But a prerequisite for this approach is that the image contrast
     within the images provided to the -se_epi option must match the b=0 volumes
     present within the input DWI series: this means equivalent TE, TR and flip
     angle (note that differences in multi-band factors between two acquisitions
     may lead to differences in TR).

EXAMPLE USAGES

     A basic DWI acquisition, where all image volumes are acquired in a single
     protocol with fixed phase encoding:
       $ dwifslpreproc DWI_in.mif DWI_out.mif -rpe_none -pe_dir ap -readout_time 0.55
     Due to use of a single fixed phase encoding, no EPI distortion correction
     can be applied in this case.

     DWIs all acquired with a single fixed phase encoding; but additionally a
     pair of b=0 images with reversed phase encoding to estimate the
     inhomogeneity field:
       $ mrcat b0_ap.mif b0_pa.mif b0_pair.mif -axis 3; dwifslpreproc DWI_in.mif DWI_out.mif -rpe_pair -se_epi b0_pair.mif -pe_dir ap -readout_time 0.72 -align_seepi
     Here the two individual b=0 volumes are concatenated into a single 4D image
     series, and this is provided to the script via the -se_epi option. Note
     that with the -rpe_pair option used here, which indicates that the SE-EPI
     image series contains one or more pairs of b=0 images with reversed phase
     encoding, the FIRST HALF of the volumes in the SE-EPI series must possess
     the same phase encoding as the input DWI series, while the second half are
     assumed to contain the opposite phase encoding direction but identical
     total readout time. Use of the -align_seepi option is advocated as long as
     its use is valid (more information in the Description section).

     All DWI directions & b-values are acquired twice, with the phase encoding
     direction of the second acquisition protocol being reversed with respect to
     the first:
       $ mrcat DWI_lr.mif DWI_rl.mif DWI_all.mif -axis 3; dwifslpreproc DWI_all.mif DWI_out.mif -rpe_all -pe_dir lr -readout_time 0.66
     Here the two acquisition protocols are concatenated into a single DWI
     series containing all acquired volumes. The direction indicated via the
     -pe_dir option should be the direction of phase encoding used in
     acquisition of the FIRST HALF of volumes in the input DWI series; ie. the
     first of the two files that was provided to the mrcat command. In this
     usage scenario, the output DWI series will contain the same number of image
     volumes as ONE of the acquired DWI series (ie. half of the number in the
     concatenated series); this is because the script will identify pairs of
     volumes that possess the same diffusion sensitisation but reversed phase
     encoding, and perform explicit recombination of those volume pairs in such
     a way that image contrast in regions of inhomogeneity is determined from
     the stretched rather than the compressed image.

     Any acquisition scheme that does not fall into one of the example usages
     above:
       $ mrcat DWI_*.mif DWI_all.mif -axis 3; mrcat b0_*.mif b0_all.mif -axis 3; dwifslpreproc DWI_all.mif DWI_out.mif -rpe_header -se_epi b0_all.mif -align_seepi
     With this usage, the relevant phase encoding information is determined
     entirely based on the contents of the relevant image headers, and
     dwifslpreproc prepares all metadata for the executed FSL commands
     accordingly. This can therefore be used if the particular DWI acquisition
     strategy used does not correspond to one of the simple examples as
     described in the prior examples. This usage is predicated on the headers of
     the input files containing appropriately-named key-value fields such that
     MRtrix3 tools identify them as such. In some cases, conversion from DICOM
     using MRtrix3 commands will automatically extract and embed this
     information; however this is not true for all scanner vendors and/or
     software versions. In the latter case it may be possible to manually
     provide these metadata; either using the -json_import command-line option
     of dwifslpreproc, or the -json_import or one of the -import_pe_* command-
     line options of MRtrix3's mrconvert command (and saving in .mif format)
     prior to running dwifslpreproc.

OPTIONS

  -pe_dir PE
     Manually specify the phase encoding direction of the input series; can be a
     signed axis number (e.g. -0, 1, +2), an axis designator (e.g. RL, PA, IS),
     or NIfTI axis codes (e.g. i-, j, k)

  -readout_time time
     Manually specify the total readout time of the input series (in seconds)

  -se_epi image
     Provide an additional image series consisting of spin-echo EPI images,
     which is to be used exclusively by topup for estimating the inhomogeneity
     field (i.e. it will not form part of the output image series)

  -align_seepi
     Achieve alignment between the SE-EPI images used for inhomogeneity field
     estimation, and the DWIs (more information in Description section)

  -json_import file
     Import image header information from an associated JSON file (may be
     necessary to determine phase encoding information)

  -topup_options " TopupOptions"
     Manually provide additional command-line options to the topup command
     (provide a string within quotation marks that contains at least one space,
     even if only passing a single command-line option to topup)

  -eddy_options " EddyOptions"
     Manually provide additional command-line options to the eddy command
     (provide a string within quotation marks that contains at least one space,
     even if only passing a single command-line option to eddy)

  -eddy_mask image
     Provide a processing mask to use for eddy, instead of having dwifslpreproc
     generate one internally using dwi2mask

  -eddy_slspec file
     Provide a file containing slice groupings for eddy's slice-to-volume
     registration

  -eddyqc_text directory
     Copy the various text-based statistical outputs generated by eddy, and the
     output of eddy_qc (if installed), into an output directory

  -eddyqc_all directory
     Copy ALL outputs generated by eddy (including images), and the output of
     eddy_qc (if installed), into an output directory

Options for specifying the acquisition phase-encoding design; note that one of the -rpe_* options MUST be provided

  -rpe_none
     Specify that no reversed phase-encoding image data is being provided; eddy
     will perform eddy current and motion correction only

  -rpe_pair
     Specify that a set of images (typically b=0 volumes) will be provided for
     use in inhomogeneity field estimation only (using the -se_epi option)

  -rpe_all
     Specify that ALL DWIs have been acquired with opposing phase-encoding

  -rpe_header
     Specify that the phase-encoding information can be found in the image
     header(s), and that this is the information that the script should use

Options for importing the diffusion gradient table

  -grad GRAD
     Provide the diffusion gradient table in MRtrix format

  -fslgrad bvecs bvals
     Provide the diffusion gradient table in FSL bvecs/bvals format

Options for exporting the diffusion gradient table

  -export_grad_mrtrix grad
     Export the final gradient table in MRtrix format

  -export_grad_fsl bvecs bvals
     Export the final gradient table in FSL bvecs/bvals format

Additional standard options for Python scripts

  -nocleanup
     do not delete intermediate files during script execution, and do not delete
     scratch directory at script completion.

  -scratch /path/to/scratch/
     manually specify the path in which to generate the scratch directory.

  -continue <ScratchDir> <LastFile>
     continue the script from a previous execution; must provide the scratch
     directory path, and the name of the last successfully-generated file.

Standard options

  -info
     display information messages.

  -quiet
     do not display information messages or progress status. Alternatively, this
     can be achieved by setting the MRTRIX_QUIET environment variable to a non-
     empty string.

  -debug
     display debugging messages.

  -force
     force overwrite of output files.

  -nthreads number
     use this number of threads in multi-threaded applications (set to 0 to
     disable multi-threading).

  -config key value  (multiple uses permitted)
     temporarily set the value of an MRtrix config file entry.

  -help
     display this information page and exit.

  -version
     display version information and exit.