Citations

Warrington S, Bryant K, Charquero-Ballester M, Douaud G, Jbabdi S*, Mars R*, Sotiropoulos SN* (in prep.) Standardised protocols for automated tractography and connectivity blueprints in the human and macaque brain.

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

 __  _______ ____      _    ____ _____ 
 \ \/ /_   _|  _ \    / \  / ___|_   _|
  \  /  | | | |_) |  / _ \| |     | |  
  /  \  | | |  _ <  / ___ \ |___  | |  
 /_/\_\ |_| |_| \_\/_/   \_\____| |_|  
 

Usage: 
    xtract -bpx <bedpostX_dir> -out <outputDir> -str <structuresFile> -p <protocolsFolder> [options]
    xtract -bpx <bedpostX_dir> -out <outputDir> -species HUMAN [options]
    xtract -bpx <bedpostX_dir> -out <outputDir> -species MACAQUE [options]

    Compulsory arguments:

       -bpx <folder>                     Path to bedpostx folder
       -out <folder>                     Path to output folder
       
       And EITHER:
       -str <file>                       Structures file (format: <tractName> [samples=1], 1 means 1000, '#' to skip lines)
       -p   <folder>                     Protocols folder (all masks in same standard space)

       Or:
       -species <SPECIES>                One of HUMAN or MACAQUE

    Optional arguments:

       -stdwarp <std2diff> <diff2std>    Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard}) 
       -gpu                              Use GPU version 
       -native                           Run tractography in native (diffusion) space
       -res <mm>                         Output resolution (Default=same as in protocol folders unless '-native' used)


Running XTRACT


Atlases

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

Tract

Abbreviation

Arcuate Fasciculus

AF

Acoustic Radiation

AR

Anterior Thalamic Radiation

ATR

Cingulum subsection : Dorsal

CBD

Cingulum subsection : Parahippocampal

CBP

Cingulum subsection : Temporal

CBT

Corticospinal Tract

CST

Frontal Aslant

FA

Forceps Major

FMA

Forceps Minor

FMI

Fornix

FX

Inferior Longitudinal Fasciculus

ILF

Inferior Fronto-Occipital Fasciculus

IFO

Middle Cerebellar Peduncle

MCP

Middle Longitudinal Fasciculuc

MdLF

Optic Radiation

OR

Superior Thalamic Radiation

STR

Superior Longitudinal Fasciculus 1

SLF1

Superior Longitudinal Fasciculus 2

SLF2

Superior Longitudinal Fasciculus 3

SLF3

Anterior Commissure

AC

Uncinate Fasciculus

UF

Vertical Occipital Fasciculus

VOF


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:

Optional:

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.


Visualising results with FSLEYES

The output of XTRACT is a folder that contrains tracts in separate folders. We provide a convenient script 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

 __  _______ ____      _    ____ _____         _                        
 \ \/ /_   _|  _ \    / \  / ___|_   _| __   _(_) _____      _____ _ __ 
  \  /  | | | |_) |  / _ \| |     | |   \ \ / / |/ _ \ \ /\ / / _ \ '__|
  /  \  | | |  _ <  / ___ \ |___  | |    \ V /| |  __/\ V  V /  __/ |   
 /_/\_\ |_| |_| \_\/_/   \_\____| |_|     \_/ |_|\___| \_/\_/ \___|_|                                                                           
                                                             

Usage:
    xtract_viewer -dir <xtractDir> [options]

    Compulsory arguments:

       -dir FOLDER                       Path to XTRACT output folder

    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

       -brain                            The brain image to use for the background overlay - must be in the same space as tracts.
                                         Default is the FSL_HCP065_FA map
 

XTRACT (last edited 12:06:52 20-08-2019 by SaadJbabdi)