Updated to reflect xtract_viewer changes

README.md

 ## XTRACT - a command-line tool for automated tractography
 
-XTRACT 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 
+XTRACT 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)
 
 The script was written by Saad Jbabdi & Stamatios Sotiropoulos
@@ -31,16 +31,16 @@ NeuroImage, 76(1), 400-411. DOI: 10.1016/j.neuroimage.2013.03.015
 
 ---------------------------------------------------------------------
 
-## Usage: 
+## Usage:
 ```
- __  _______ ____      _    ____ _____ 
+ __  _______ ____      _    ____ _____
  \ \/ /_   _|  _ \    / \  / ___|_   _|
   \  /  | | | |_) |  / _ \| |     | |  
   /  \  | | |  _ <  / ___ \ |___  | |  
  /_/\_\ |_| |_| \_\/_/   \_\____| |_|  
- 
 
-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]
@@ -49,7 +49,7 @@ Usage:
 
        -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)
@@ -59,8 +59,8 @@ Usage:
 
     Optional arguments:
 
-       -stdwarp <std2diff> <diff2std>    Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard}) 
-       -gpu                              Use GPU version 
+       -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)
        -ptx_options <options.txt>	     Pass extra probtrackx2 options as a text file to override defaults, e.g. --steplength=0.2 --distthresh=10)
@@ -70,8 +70,8 @@ Usage:
 ---------------------------------------------------------------------
 
 ## Running XTRACT:
-  XTRACT automatically detects if $SGE_ROOT is set and if so uses FSL_SUB. 
-  For optimal performance, use the GPU version!!!! 
+  XTRACT automatically detects if $SGE_ROOT is set and if so uses FSL_SUB.
+  For optimal performance, use the GPU version!!!!
 
 ---------------------------------------------------------------------
 
@@ -80,7 +80,7 @@ Usage:
 - 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:
@@ -119,12 +119,12 @@ When running XTRACT with the '-species' option, a predefined list of tracts is a
 
 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. 
+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 
+- seed.nii.gz : a seed mask
 
 **Optional**:
 - stop.nii.gz    : a stop mask if required
@@ -133,7 +133,7 @@ Then create the following NIFTI files (with this exact naming) and copy them int
   - 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 
+  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.
 
@@ -146,27 +146,33 @@ The output of XTRACT is a folder that contrains tracts in separate folders. We p
 
 ```
  __  _______ ____      _    ____ _____         _                        
- \ \/ /_   _|  _ \    / \  / ___|_   _| __   _(_) _____      _____ _ __ 
+ \ \/ /_   _|  _ \    / \  / ___|_   _| __   _(_) _____      _____ _ __
   \  /  | | | |_) |  / _ \| |     | |   \ \ / / |/ _ \ \ /\ / / _ \ '__|
   /  \  | | |  _ <  / ___ \ |___  | |    \ V /| |  __/\ V  V /  __/ |   
  /_/\_\ |_| |_| \_\/_/   \_\____| |_|     \_/ |_|\___| \_/\_/ \___|_|                                                                           
-                                                             
 
-Usage:
-    xtract_viewer -dir <xtractDir> [options]
 
-    Compulsory arguments:
+ Usage:
+     xtract_viewer -dir <xtractDir> -species HUMAN [options]
+     xtract_viewer -dir <xtractDir> -species MACAQUE [options]
+     xtract_viewer -dir <xtractDir> -brain <PATH> [options]
 
-       -dir FOLDER                       Path to XTRACT output folder
+     Compulsory arguments:
 
-    Optional 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
 
-       -str STRUCTURE,STRUCTURE,...     Structures (comma separated (default = display all that is found in input folder)
+     Optional arguments:
 
-       -thr NUMBER NUMBER                The lower and upper thresholds applied to the tracts for viewing
-                                         Default = 0.001 0.1
+        -str STRUCTURE,STRUCTURE,...      Structures (comma separated (default = display all that is found in input folder)
 
-       -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
+        -thr NUMBER NUMBER                The lower and upper thresholds applied to the tracts for viewing
+                                          Default = 0.001 0.1
 
 ```