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Update help in README.md
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draffelt committed Feb 6, 2017
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Expand Up @@ -60,9 +60,9 @@ DESCRIPTION
Density & Cross-section). The analysis pipeline relies primarily on the
MRtrix3 software package (www.mrtrix.org).
Options for the population_template script
optional arguments
--participant_label PARTICIPANT_LABEL
--participant_label <space-separated list>
The label(s) of the participant(s) that should be analyzed. The label
corresponds to sub-<participant_label> from the BIDS spec (so it does not
include "sub-"). If this parameter is not provided all subjects should be
Expand All @@ -73,6 +73,28 @@ Options for the population_template script
The number of CPU cores available on the compute node. Set to 0 to use the
maximum number of cores available
Options for this Fibre Density and Cross-section BIDS-App
-vox_size FLOAT
define the voxel size (in mm) to be used during the upsampling step
(participant1 analysis level only)
-group_subset GROUP_SUBSET
Define a subset of participants to be used when generating the group-
average FOD template and response functions. The subset is to be supplied
as a comma separate list. Note the subset should be representable of your
entire population and not biased towards one particular group. For example
in a patient-control comparison, choose equal numbers of patients and
controls. Used in group1 and group2 analysis levels.
-num_tracks INT
define the number of streamlines to be computed when performing
tractography on the FOD template. (group3 analysis level only)
-num_tracks_sift INT
define the number of streamlines to remain after performing SIFT on the
tractogram(group3 analysis level only)
Standard options
-continue <TempDir> <LastFile>
Expand All @@ -85,18 +107,15 @@ Standard options
-help
Display help information for the script
-nocleanup
Do not delete temporary files during script, or temporary directory at
script completion
-tempdir /path/to/tmp/
Manually specify the path in which to generate the temporary directory
-quiet
Suppress all console output during script execution
-verbose
Display additional information for every command invoked
Display additional information and progress for every command invoked
-debug
Display additional debugging information over and above the verbose output
AUTHOR
David Raffelt (david.raffelt@florey.edu.au)
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