From 81c11e7701c658a410257f8f74476628db5deb3c Mon Sep 17 00:00:00 2001
From: Stephen Smith <steve@fmrib.ox.ac.uk>
Date: Sun, 12 Mar 2006 16:14:54 +0000
Subject: [PATCH] added --tglobal option and fixed offset for --tcustom option
---
slicetimer.cc | 32 +++++++++++++++++++-------------
1 file changed, 19 insertions(+), 13 deletions(-)
diff --git a/slicetimer.cc b/slicetimer.cc
index 3698768..ab14ef5 100644
--- a/slicetimer.cc
+++ b/slicetimer.cc
@@ -41,7 +41,7 @@ Option<bool> odd(string("--odd"), false,
string("use interleaved acquisition"),
false, no_argument);
Option<bool> down(string("--down"), false,
- string("reverse slice indexing"),
+ string("reverse slice indexing (default is: slices were acquired bottom-up)"),
false, no_argument);
Option<string> inputname(string("-i,--in"), string(""),
string("filename of input timeseries"),
@@ -52,6 +52,9 @@ Option<string> outputname(string("-o,--out"), string(""),
Option<string> tcustom(string("--tcustom"), string(""),
string("filename of single-column custom interleave timing file"),
false, requires_argument);
+Option<float> tglobal(string("--tglobal"), 0.5,
+ string("global shift (default is 0.5 = no shift)"),
+ false, requires_argument);
Option<string> ocustom(string("--ocustom"), string(""),
string("filename of single-column custom interleave order file (first slice is referred to as 1 not 0)"),
false, requires_argument);
@@ -106,45 +109,47 @@ int do_slice_correction()
ColumnVector userkernel = sinckernel1D("hanning", 7, 1201);
// for(int i=1; i<=1201; i++) cout << i << " " << userkernel(i) << endl;
- float recenter = (((float) no_slices)/2 - 0.5)/ no_slices;
+ float recenter = (((float) no_slices)/2 - 0.5)/ no_slices; // only valid for slice-count-based corrections
for (int slice=1; slice<=no_slices; slice++) {
- if (tcustom.set()) {
- offset = -timings(slice, 1);
+ if (tglobal.set()) {
+ offset = 0.5 - tglobal.value();
+ } else if (tcustom.set()) {
+ offset = 0.5 - timings(slice, 1);
} else if (ocustom.set()) {
int local_count=1;
while (local_count <= no_slices) {
if (timings(local_count, 1) == slice) {
- offset = -(local_count -1)* (slice_spacing / repeat_time);
+ offset = recenter -(local_count -1)* (slice_spacing / repeat_time);
local_count = no_slices + 1;
} else
local_count++;
}
} else if (odd.value()) { // acquisition order: 1,3,5, ..., 2,4,6 ...
if ((slice % 2) == 0) // even
- offset = -( ceil((float)no_slices / 2) + ((slice -1)/ 2)) * (slice_spacing / repeat_time);
+ offset = recenter - ( ceil((float)no_slices / 2) + ((slice -1)/ 2)) * (slice_spacing / repeat_time);
else
- offset = -((slice -1) / 2) * (slice_spacing / repeat_time);
+ offset = recenter - ((slice -1) / 2) * (slice_spacing / repeat_time);
} else if (down.value()) {
- offset = -(no_slices - slice)* (slice_spacing / repeat_time);
+ offset = recenter - (no_slices - slice) * (slice_spacing / repeat_time);
} else {
- offset = -(slice -1)* (slice_spacing / repeat_time);
+ offset = recenter - (slice -1) * (slice_spacing / repeat_time);
}
-
+
for (int x_pos = 0; x_pos < timeseries. xsize(); x_pos++)
for (int y_pos = 0; y_pos < timeseries. ysize(); y_pos++){
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, 7);
+ // interpseries(time_step) = interpolate_1d(voxeltimeseries, time_step - offset);
+ interpseries(time_step) = kernelinterpolation_1d(voxeltimeseries, time_step - offset, userkernel, 7);
}
timeseries.setvoxelts(interpseries,x_pos,y_pos,slice-1);
}
if (verbose.value())
- cerr << "Slice " << slice << " offset " << offset + recenter << endl;
+ cerr << "Slice " << slice << " offset " << offset << endl;
}
if (direction.value() == 1) timeseries. swapdimensions(3,2,1); // reverse Flip z and x
@@ -170,6 +175,7 @@ int main (int argc,char** argv)
options.add(direction);
options.add(odd);
options.add(tcustom);
+ options.add(tglobal);
options.add(ocustom);
options.parse_command_line(argc, argv);
--
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