From 1fbb0b8d8cf6a582fb42c5bc963cf990ae621560 Mon Sep 17 00:00:00 2001
From: Christian Beckmann <c.beckmann@donders.ru.nl>
Date: Thu, 11 Dec 2008 23:43:35 +0000
Subject: [PATCH] new option to fsl_sbca
---
fsl_sbca.cc | 48 +++++++++++++++++++++++++++++++++++++-----------
1 file changed, 37 insertions(+), 11 deletions(-)
diff --git a/fsl_sbca.cc b/fsl_sbca.cc
index e0cd66e..bee6160 100644
--- a/fsl_sbca.cc
+++ b/fsl_sbca.cc
@@ -37,7 +37,7 @@ using namespace std;
string("output file base name"),
true, requires_argument);
Option<string> fnseed(string("-s,--seed"), string(""),
- string("seed voxel coordinate or file name of seed mask (3D file)"),
+ string("seed voxel coordinate or file name of seed mask (3D/4D file)"),
true, requires_argument);
Option<string> fntarget(string("-t,--target"), string(""),
string("file name of target mask(s) (3D or 4D file)"),
@@ -48,6 +48,9 @@ using namespace std;
Option<string> fnconf(string("--conf"), string(""),
string(" file name (or comma-separated list of file name) for confound ascii txt files"),
false, requires_argument);
+ Option<string> fnseeddata(string("--seeddata"), string(""),
+ string("file name of 4D data file for the seed"),
+ false, requires_argument);
Option<bool> map_bin(string("--bin"), false,
string(" binarise spatial maps prior to calculation of time courses"),
false, no_argument);
@@ -177,9 +180,12 @@ void create_mask(string what){
void create_seeds(string what){
if(debug.value())
cerr << "DBG: in create_seeds" << endl;
-
+
+
+ volume4D<float> tmp_vol;
if(fsl_imageexists(what)){
- read_volume(maskS,what);
+ read_volume4D(tmp_vol,what);
+ maskS = tmp_vol[0];
if(!samesize(orig_data[0],maskS)){
cerr << "ERROR: Seed mask image does not match input image" << endl;
exit(1);
@@ -187,17 +193,36 @@ void create_seeds(string what){
}
else
create_mask(what);
-
- volume4D<float> tmp_mask;
- tmp_mask.addvolume(maskS);
- maskS.binarise(1e-8);
- Matrix scales = tmp_mask.matrix(maskS);
- seeds = remmean(orig_data.matrix(maskS),1);
- if(!map_bin.value())
- seeds = SP(seeds, ones(seeds.Nrows(),1) * scales);
+ if(tmp_vol.tsize() > 1 && tmp_vol.tsize() == orig_data.tsize()){
+ maskS *= tmp_vol[0] / tmp_vol.tsize();
+ for(int ctr=1; ctr < tmp_vol.tsize(); ctr++)
+ maskS += tmp_vol[ctr] * tmp_vol[ctr] / tmp_vol.tsize();
+ maskS.binarise(1e-8);
+ seeds = remmean(tmp_vol.matrix(maskS),1);
+ }
+ else{
+ volume4D<float> tmp_mask;
+ tmp_mask.addvolume(maskS);
+ maskS.binarise(1e-8);
+
+ if(fnseeddata.value()>"" && fsl_imageexists(fnseeddata.value())){
+ volume4D<float> seed_data;
+ if(verbose.value())
+ cout << " Reading input data for seeds " << fnseeddata.value() << endl;
+ read_volume4D(seed_data,fnseeddata.value());
+ seeds = remmean(seed_data.matrix(maskS),1);
+ }else{
+ seeds = remmean(orig_data.matrix(maskS),1);
+ if(!map_bin.value()){
+ Matrix scales = tmp_mask.matrix(maskS);
+ seeds = SP(seeds, ones(seeds.Nrows(),1) * scales);
+ }
+ }
+ }
voxels = seeds.Ncols();
+
if(debug.value()){
cerr << "DBG: " << voxels << " voxels" << endl;
cerr << "DBG: seeds matrix is " << seeds.Nrows() << " x " << seeds.Ncols() << endl;
@@ -487,6 +512,7 @@ int main(int argc,char *argv[]){
options.add(fntarget);
options.add(regress_only);
options.add(fnconf);
+ options.add(fnseeddata);
options.add(map_bin);
options.add(tc_mean);
options.add(tc_order);
--
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