Commit 7087366e authored by Shaun Warrington's avatar Shaun Warrington
Browse files

Reflecting changes in main script

parent 3583e9bd
......@@ -46,19 +46,24 @@ NeuroImage, 76(1), 400-411. DOI: 10.1016/j.neuroimage.2013.03.015
Compulsory arguments:
-bpx <folder> Path to bedpostx folder
-out <folder> Path to output folder
-species <SPECIES> One of HUMAN or MACAQUE
-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=$FSLDIR/etc/xtract_data/<SPECIES>)
-stdwarp <std2diff> <diff2std> Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard})
-gpu Use GPU version
-native Run tractography in native (diffusion) space
-res <mm> Output resolution (Default=same as in protocol folders unless '-native' used)
-ptx_options <options.txt> Pass extra probtrackx2 options as a text file to override defaults, e.g. --steplength=0.2 --distthresh=10)
-list List the tract names used in XTRACT
-str <file> Structures file (format: <tractName> per line OR format: <tractName> [samples=1], 1 means 1000, '#' to skip lines)
-p <folder> Protocols folder (all masks in same standard space) (Default=$FSLDIR/etc/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
```
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