From 7a2702de49514c76bfcc5301117d3f953ad23ecf Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Mon, 23 Nov 2009 09:45:27 +0000
Subject: [PATCH] prepare for 4.1.5
---
bedpostx | 3 +--
diffmodels.cc | 32 ++++++++++----------------------
xfibresoptions.h | 2 +-
3 files changed, 12 insertions(+), 25 deletions(-)
diff --git a/bedpostx b/bedpostx
index cd73f6d..f56d0c4 100755
--- a/bedpostx
+++ b/bedpostx
@@ -24,7 +24,6 @@ Usage() {
echo "-b (burnin period, default 1000)"
echo "-j (number of jumps, default 1250)"
echo "-s (sample every, default 25)"
- echo "-model (1:monoexponential [default] - 2:non-monoexponential [to be used in multi-shell acquisitions])"
echo ""
exit 1
}
@@ -188,7 +187,7 @@ bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -M $m
echo Queuing post processing stage
mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -T 60 -m as -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`
-#[ "x$SGE_ROOT" = "x" ] && kill -USR1 $monitorpid
+[ "x$SGE_ROOT" = "x" ] && kill -USR1 $monitorpid
if [ "x$SGE_ROOT" != "x" ]; then
echo
diff --git a/diffmodels.cc b/diffmodels.cc
index 78e052e..670c888 100644
--- a/diffmodels.cc
+++ b/diffmodels.cc
@@ -449,7 +449,7 @@ void PVM_single::fit(){
ColumnVector start(nparams);
start(1) = dti.get_s0();
start(2) = dti.get_md()>0?dti.get_md()*2:0.001; // empirically found that d~2*MD
- start(3) = f2x(dti.get_fa()); // first pvf = FA
+ start(3) = dti.get_fa()<1?f2x(dti.get_fa()):f2x(0.95); // first pvf = FA
start(4) = _th;
start(5) = _ph;
float sumf=x2f(start(2));
@@ -725,34 +725,22 @@ void PVM_multi::fit(){
DTI dti(Y,bvecs,bvals);
dti.linfit();
- // set starting parameters for nonlinear fitting
- float _th,_ph;
- cart2sph(dti.get_v1(),_th,_ph);
+ // initialise with simple pvm
+ PVM_single pvm1(Y,bvecs,bvals,nfib);
+ pvm1.fit();
float _a,_b;
_a = 1; // start with d=d_std
- _b = dti.get_md()>0?dti.get_md()*2:0.001;
+ _b = pvm1.get_d();
ColumnVector start(nparams);
- start(1) = dti.get_s0();
+ start(1) = pvm1.get_s0();
start(2) = _a;
start(3) = _b;
- start(4) = f2x(dti.get_fa()); // first pvf = FA
- start(5) = _th;
- start(6) = _ph;
- float sumf=x2f(start(2));
- float tmpsumf=sumf;
- for(int ii=2,i=7;ii<=nfib;ii++,i+=3){
- float denom=2;
- do{
- start(i) = f2x(x2f(start(i-3))/denom);
- denom *= 2;
- tmpsumf = sumf + x2f(start(i));
- }while(tmpsumf>=1);
- sumf += x2f(start(i));
- cart2sph(dti.get_v(ii),_th,_ph);
- start(i+1) = _th;
- start(i+2) = _ph;
+ for(int i=1,ii=4;i<=nfib;i++,ii+=3){
+ start(ii) = pvm1.get_f(i);
+ start(ii+1) = pvm1.get_th(i);
+ start(ii+2) = pvm1.get_ph(i);
}
// do the fit
diff --git a/xfibresoptions.h b/xfibresoptions.h
index 0b0ad77..5ae705d 100644
--- a/xfibresoptions.h
+++ b/xfibresoptions.h
@@ -36,7 +36,7 @@ class xfibresOptions {
Option<string> bvecsfile;
Option<string> bvalsfile;
Option<int> nfibres;
- Option<int> modelnum;
+ FmribOption<int> modelnum;
Option<float> fudge;
Option<int> njumps;
Option<int> nburn;
--
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