From 57dc7f9cf8cd5ba98b78648c31887a17f496016e Mon Sep 17 00:00:00 2001
From: Stephen Smith <steve@fmrib.ox.ac.uk>
Date: Fri, 6 Sep 2002 18:10:22 +0000
Subject: [PATCH] *** empty log message ***
---
slicetimer.cc | 28 +++++++++++++---------------
1 file changed, 13 insertions(+), 15 deletions(-)
diff --git a/slicetimer.cc b/slicetimer.cc
index 4218876..995fa4c 100644
--- a/slicetimer.cc
+++ b/slicetimer.cc
@@ -55,7 +55,7 @@ Option<string> tcustom(string("--tcustom"), string(""),
string("filename of single-column custom interleave timing file"),
false, requires_argument);
Option<string> ocustom(string("--ocustom"), string(""),
- string("filename of single-column custom interleave order file"),
+ string("filename of single-column custom interleave order file (first slice is referred to as 1 not 0)"),
false, requires_argument);
Option<int> direction(string("-d,--direction"), 3,
string("direction of slice acquisition (x=1,y=2,z=3) - default is z"),
@@ -68,11 +68,10 @@ int do_slice_correction()
{
volume4D<float> timeseries;
volumeinfo in_info;
- ColumnVector voxeltimeseries, interpseries;
Matrix timings;
int no_volumes, no_slices;
- float repeat_time, offset, slice_spacing, recenter;
+ float repeat_time, offset=0, slice_spacing;
if (inputname.set()) {
if (verbose.value()) { cout << "Reading input volume" << endl; }
@@ -106,16 +105,13 @@ int do_slice_correction()
timings = read_ascii_matrix(ocustom.value(), timeseries.zsize(), 1);
}
- offset = 0.0;
-
ColumnVector userkernel = sinckernel1D("hanning", 7, 1201);
-
- // if (down.value())
- // recenter = (((float) no_slices)/2 + 0.5)/ no_slices;
- //else
- recenter = (((float) no_slices)/2 - 0.5)/ no_slices;
+ // for(int i=1; i<=1201; i++) cout << i << " " << userkernel(i) << endl;
+
+ float recenter = (((float) no_slices)/2 - 0.5)/ no_slices;
for (int slice=1; slice<=no_slices; slice++) {
+
if (tcustom.set()) {
offset = -timings(slice, 1);
} else if (ocustom.set()) {
@@ -140,15 +136,17 @@ int do_slice_correction()
for (int x_pos = 0; x_pos < timeseries. xsize(); x_pos++)
for (int y_pos = 0; y_pos < timeseries. ysize(); y_pos++){
- voxeltimeseries = timeseries.voxelts(x_pos,y_pos,slice-1);
- interpseries = voxeltimeseries;
- for (int time_step=1; time_step <= no_volumes; time_step++)
- interpseries(time_step) = interpolate_1d(voxeltimeseries, time_step + offset + recenter);
+ ColumnVector voxeltimeseries = timeseries.voxelts(x_pos,y_pos,slice-1);
+ ColumnVector interpseries = voxeltimeseries;
+ for (int time_step=1; time_step <= no_volumes; time_step++){
+ // interpseries(time_step) = interpolate_1d(voxeltimeseries, time_step + offset + recenter);
+ interpseries(time_step) = kernelinterpolation_1d(voxeltimeseries, time_step + offset + recenter, userkernel, 3);
+ }
timeseries.setvoxelts(interpseries,x_pos,y_pos,slice-1);
}
if (verbose.value())
- cerr << "Slice / Offset (s) " << slice << " / " << offset *repeat_time * -1 << endl;
+ cerr << "Slice " << slice << " offset " << offset + recenter << endl;
}
if (direction.value() == 1) timeseries. swapdimensions(3,2,1); // reverse Flip z and x
--
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