README 2.76 KB
Newer Older
Saad Jbabdi's avatar
Saad Jbabdi committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65

---------------------------------------------------------------------
xtract is a command-line tool for running automated tractography.

Written by Saad Jbabdi & Stamatios Sotiropoulos
(based on the autoPtx tool by Marius de Groot)

---------------------------------------------------------------------
Citations:
	
de Groot, Marius; Vernooij, Meike W.; Klein, Stefan; Ikram, M. Arfan; Vos, Frans M.; Smith, Stephen M.; Niessen, Wiro J.; Andersson, Jesper L. R.(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

Warrington et al. in prep

---------------------------------------------------------------------

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)

---------------------------------------------------------------------

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 'protocols/mytrack' within the protocols folder. 

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

[Compulsory]:
- seed.nii.gz : a seed mask in MNI152 space

[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