From ed25ff5ca893e6620fc7efb2fc0697c04647b656 Mon Sep 17 00:00:00 2001 From: Dave Raffelt Date: Mon, 6 Feb 2017 17:11:38 +1000 Subject: [PATCH] Update help in README.md --- README.md | 39 +++++++++++++++++++++++++++++---------- 1 file changed, 29 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 482b6c1..b66fdfb 100644 --- a/README.md +++ b/README.md @@ -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 The label(s) of the participant(s) that should be analyzed. The label corresponds to sub- from the BIDS spec (so it does not include "sub-"). If this parameter is not provided all subjects should be @@ -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 @@ -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)