• XTRACT

XTRACT - a command-line tool for automated tractography

XTRACT (cross-species tractography) can be used to automatically extract a set of carefully dissected tracts in humans and macaques (other species to come). It can also be used to define one's own tractography protocols where all the user needs to do is to define a set of masks in standard space (e.g. MNI152)

XTRACT reads the standard space protocols and performs probabilistic tractography (probtrackx2) in the subject's native space. Resultant tracts may be stored in either the subject's native space or in standard space. The user must provide the crossing fibres fitted data (bedpostx) and diffusion to standard space registration warp fields (and their inverse).

Citations

Warrington S, Bryant K, Khrapitchev A, Sallet J, Charquero-Ballester M, Douaud G, Jbabdi S*, Mars R*, Sotiropoulos SN* (2020) XTRACT - Standardised protocols for automated tractography and connectivity blueprints in the human and macaque brain. NeuroImage. DOI: 10.1016/j.neuroimage.2020.116923

de Groot M; Vernooij MW. Klein S, Ikram MA, Vos FM, Smith SM, Niessen WJ, Andersson JLR (2013) Improving alignment in Tract-based spatial statistics: Evaluation and optimization of image registration. NeuroImage, 76(1), 400-411. DOI: 10.1016/j.neuroimage.2013.03.015

Usage

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 Usage:
     xtract -bpx <bedpostX_dir> -out <outputDir> -species <SPECIES> [options]
     xtract -list

     Compulsory arguments:

        -bpx <folder>                          Path to bedpostx folder
        -out <folder>                          Path to output folder
        -species <SPECIES>                     One of HUMAN or MACAQUE

     Optional arguments:
        -list                                  List the tract names used in XTRACT
        -str <file>                            Structures file (format: <tractName> per line OR format: <tractName> [samples=1], 1 means 1000, '#' to skip lines)
        -p <folder>                            Protocols folder (all masks in same standard space) (Default=$FSLDIR/data/xtract_data/<SPECIES>)
        -stdwarp <std2diff> <diff2std>         Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard})
        -gpu                                   Use GPU version
        -res <mm>                              Output resolution (Default=same as in protocol folders unless '-native' used)
        -ptx_options <options.txt>                 Pass extra probtrackx2 options as a text file to override defaults, e.g. --steplength=0.2 --distthresh=10)

        And EITHER:
        -native                                Run tractography in native (diffusion) space

        OR:
        -ref <refimage> <diff2ref> <ref2diff>  Reference image for running tractography in reference space, Diff2Reference and Reference2Diff transforms

Running XTRACT

XTRACT automatically detects if $SGE_ROOT is set and if so uses FSL_SUB. For optimal performance, use the GPU version!!!!

Outputs of XTRACT

Under <outputDir>:

• "commands.txt" - XTRACT processing commands
• "logs" - directory containing the probtrackx log files
• "tracts" - directory continaing tractography results

  • "<tractName>" - directory per tract, each continaing:

    • "waytotal" - txt file continaing the number of valid streamlines
    • "density.nii.gz" - nifti file containing the fibre probability distribution
    • "density_lenths.nii.gz" - nifti file containing the fibre lengths, i.e. each voxel is the average streamline length - this is the "-ompl" probtrackx option
    • "densityNorm.nii.gz" - nifti file continaing the waytotal normalised fibre probability distribution (the "density.nii.gz" divided by the total number of valid streamlines)
    • if the protocol calls for reverse-seeding:
      • "tractsInv" - directory continaing the above for the seed-target reversed run
      • "sum_waytotal" and "sum_density.nii.gz" - the summed waytotal and fibre probability distribution

If the "-native" option is being used:

• "masks" - directory

  • "<tractName>" - directory per tract continaing the native space protocol masks

The primary output is the "densityNorm.nii.gz" file.

Pre-processing

Prior to running XTRACT, you must complete the FDT processing pipeline:

1. Brain extraction using BET

2. Susceptibility distortion correction using topup (only if spin-echo fieldmaps have been acquired - if you don't have these, skip to step 3)

3. Eddy current distortion and motion correction using eddy

4. Fit the crossing fibre model using bedpostx

5. Registration to standard space (MNI152), see the FDT pipeline

Your data should now be ready to run XTRACT!

Atlases

• For HUMAN, XTRACT uses the MNI152 standard space in $FSLDIR/etc/standard

• For MACAQUE, XTRACT uses the F99 atlas in Caret - see http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases

  • We also provide a copy of the F99 atlas in $FSLDIR/etc/xtract_data/standard/F99. This includes a helper script for registering your own diffusion/structural data to the F99 altas

When running XTRACT with the '-species' option, a predefined list of tracts is automatically extracted. Currently the following tracts are available:

Adding your own tracts

Suppose you want to create an automated protocol for a tract called 'mytrack'.

First you need to create a folder called 'mytrack' which you can add e.g. in the protocols folder.

Then create the following NIFTI files (with this exact naming) and copy them into mytrack:

Compulsory:

• seed.nii.gz : a seed mask

Optional:

• stop.nii.gz : a stop mask if required
• exclude.nii.gz : an exclusion mask if required
• ONE of the following:
  • target.nii.gz : a single target mask
  • target1.nii.gz, target2.nii.gz, etc. : a number of targets, in which case streamlines will be kept if they cross ALL of them

• invert (empty file to indicate that a seed->target and target->seed run will be added and combined)

  • if such an option is required a single "target.nii.gz" file is also expected

All the masks above should be in standard space (e.g. MNI152 or F99) if you want to run the same tracking for a collection of subjects.

Next, make a structure file using the format <tractName> <nsamples> per line and call XTRACT using -species <SPECIES> -str <file> -p <folder>, pointing to your new protocols folder 'mytrack'.

Visualising results with FSLEYES

The output of XTRACT is a folder that contrains tracts in separate folders. We provide a convenient script ("xtract_viewer") that can load these tracts (or a subset of the tracts) into FSLEYES using different colours for the different tracts but matching the left/right colours.

Notice that in the FSL 6.0.2 release, "xtract_viewer" has not been included into the main $FSLDIR/bin path of executables, therefore it needs to be manually launched from

$FSLDIR/src/xtract/xtract_viewer

This has been corrected in FSL 6.0.3+

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 /_/\_\ |_| |_| \_\/_/   \_\____| |_|     \_/ |_|\___| \_/\_/ \___|_|


 Usage:
     xtract_viewer -dir <xtractDir> -species HUMAN [options]
     xtract_viewer -dir <xtractDir> -species MACAQUE [options]
     xtract_viewer -dir <xtractDir> -brain <PATH> [options]

     Compulsory arguments:

        -dir <FOLDER>                     Path to XTRACT output folder

        And EITHER:
        -species <SPECIES>                One of HUMAN or MACAQUE

        OR:
        -brain <PATH>                     The brain image to use for the background overlay - must be in the same space as tracts.
                                          Default is the FSL_HCP065_FA map for HUMAN and F99 T1 brain for MACAQUE

     Optional arguments:

        -str STRUCTURE,STRUCTURE,...      Structures (comma separated (default = display all that is found in input folder)

        -thr NUMBER NUMBER                The lower and upper thresholds applied to the tracts for viewing
                                          Default = 0.001 0.1

Extracting tract-wise summary statistics

A common usage of the XTRACT output is to summarise tracts in terms of simple summary statistics, such as their volume and microstructural properties (e.g. mean FA). We provide XTRACT stats to get such summary statistics in a quick and simple way.

You can use XTRACT stats with any modelled diffusion data, e.g. DTI, bedpostx, DKI.

Simply provide; the directory (and basename of files, if any) leading to the diffusion data of interest, the directory containing the XTRACT output, the warp field (or use 'native' if tracts are already in diffusion space). If tracts are not in diffusion space, you must also provide a reference image in diffusion space (e.g. FA map).

e.g. call: xtract_stats -d /home/DTI/dti_ -xtract /home/xtract -w /home/warp/standard2diff -r /home/DTI/dti_FA

The output (a .csv file) by default contains the tract volume (mm3) and the mean, median and standard deviation of the probability, length, FA and MD for each tract.

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\ \/ /_   _|  _ \    / \  / ___|_   _|__| |_ __ _| |_ ___
 \  /  | | | |_) |  / _ \| |     | |/ __| __/ _  | __/ __|
 /  \  | | |  _ <  / ___ \ |___  | |\__ \ || (_| | |_\__ \
/_/\_\ |_| |_| \_\/_/   \_\____| |_||___/\__\__ _|\__|___/


Usage:
    xtract_stats -d <dir_basename> -xtract <XTRACT_dir> -w <xtract2diff> [options]

    Compulsory arguments:

       -d <folder_basename>                   Path to microstructure folder and basename of data (e.g. /home/DTI/dti_)
       -xtract <folder>                       Path to XTRACT output folder
       -w <xtract2diff>                       EITHER XTRACT results to diffusion space transform OR 'native' if tracts are already in diffusion space

    Optional arguments:
       -r <reference>                         If not 'native', provide reference image in diffusion space (e.g. /home/DTI/dti_FA)
       -out <path>                            Output filepath (Default <XTRACT_dir>/stats.csv)
       -str <file>                            Structures file (as in XTRACT) (Default is all tracts under <XTRACT_dir>)
       -thr <float>                           Threshold applied to tract probability map (default = 0.001 = 0.1%)

       -meas <list>                           Comma separated list of features to extract (Default = vol,prob,length,FA,MD - assumes DTI folder has been provided)
                                              vol = tract volume, prob = tract probability, length = tract length
                                              Additional metrics must follow file naming conventions. e.g. for dti_L1 use 'L1'

       -keepfiles                             Keep temporary files