From 75c8c0023d551d352c488fe9de355d215c4513ea Mon Sep 17 00:00:00 2001
From: Stamatios Sotiropoulos <stam@fmrib.ox.ac.uk>
Date: Mon, 30 Jan 2012 15:18:10 +0000
Subject: [PATCH] New options: Noise floor, Ball&Binghams, Fanning estimates
from ball&stick
---
pvmfitOptions.h | 32 ++++++++++++++++++++++++++------
1 file changed, 26 insertions(+), 6 deletions(-)
diff --git a/pvmfitOptions.h b/pvmfitOptions.h
index 8b023c3..f9fed09 100644
--- a/pvmfitOptions.h
+++ b/pvmfitOptions.h
@@ -36,8 +36,12 @@ class pvmfitOptions {
Option<string> bvalsfile;
Option<int> nfibres;
Option<int> modelnum;
- Option<bool> include_f0;
+ Option<bool> all;
Option<bool> cnonlinear;
+ Option<bool> cnonlinear_Fanning;
+ Option<bool> gridsearch;
+ Option<bool> use_f0;
+ Option<bool> saveBIC;
bool parse_command_line(int argc, char** argv);
@@ -85,13 +89,25 @@ class pvmfitOptions {
string("number of fibres to fit - default=1"),
false, requires_argument),
modelnum(string("--model"), 1,
- string("\t1:monoexponential;2:non mono-exponential"),
+ string("\t1:Ball-Sticks (single-shell); 2:Ball-Sticks (multi-shells); 4:Ball-Binghams"),
false, requires_argument),
- include_f0(string("--f0"),false,
- string("\tInclude noise floor in the model (default=false)"),
+ all(string("--all"),false,
+ string("\tFanning models: Fit all models from 1 up to N fibres and choose the best using BIC"),
false,no_argument),
cnonlinear(string("--cnonlinear"),false,
- string("Apply constrained nonlinear optimization on diffusivity, volume fractions (model1)"),
+ string("Model1: Apply constrained nonlinear optimization on the diffusivity, volume fractions and their sum"),
+ false,no_argument),
+ cnonlinear_Fanning(string("--cnonlinear_F"),false,
+ string("Model1: Apply constrained nonlinear optimization on the diffusivity, volume fractions and their sum.\n\t\t\tReturn n fanning angle estimates, using the Hessian of the cost function"),
+ false,no_argument),
+ gridsearch(string("--gridsearch"),false,
+ string("Use grid search (on the fanning eigenvalues). Default=off"),
+ false,no_argument),
+ use_f0(string("--f0"),false,
+ string("\tInclude noise floor parameter in the model"),
+ false,no_argument),
+ saveBIC(string("--BIC"),false,
+ string("\tSave BIC for certain models"),
false,no_argument),
options("pvmfit", "pvmfit -k <datafile> -m <maskfile> -r <bvecsfile> -b <bvalsfile> [-n 2]\n")
{
@@ -107,8 +123,12 @@ class pvmfitOptions {
options.add(bvalsfile);
options.add(nfibres);
options.add(modelnum);
- options.add(include_f0);
+ options.add(all);
options.add(cnonlinear);
+ options.add(cnonlinear_Fanning);
+ options.add(gridsearch);
+ options.add(use_f0);
+ options.add(saveBIC);
}
catch(X_OptionError& e) {
options.usage();
--
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