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mrconvert PE export with -coord option #1022

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Merged
Lestropie merged 2 commits into from
Jun 20, 2017
Merged

mrconvert PE export with -coord option #1022

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4003156
mrconvert: Fix export_pe with -coord option.
dchristiaens Jun 20, 2017
672b56c
Merge branch 'master' of github.com:MRtrix3/mrtrix3
dchristiaens Jun 20, 2017
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5 changes: 3 additions & 2 deletions cmd/mrconvert.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -317,8 +317,9 @@ void run ()
if (*maxval >= header_in.size(axis))
throw Exception ("coordinate position " + str(*maxval) + " for axis " + str(axis) + " provided with -coord option is out of range of input image");

header_out.size (axis) = pos[axis].size();
if (axis == 3) {
const auto grad = DWI::get_DW_scheme (header_out);
const auto grad = DWI::get_DW_scheme (header_in);
if (grad.rows()) {
if ((ssize_t)grad.rows() != header_in.size(3)) {
WARN ("Diffusion encoding of input file does not match number of image volumes; omitting gradient information from output image");
Expand All @@ -332,7 +333,7 @@ void run ()
}
Eigen::MatrixXd pe_scheme;
try {
pe_scheme = PhaseEncoding::parse_scheme (header_out);
pe_scheme = PhaseEncoding::get_scheme (header_in);
if (pe_scheme.rows()) {
Eigen::MatrixXd extract_scheme (pos[3].size(), pe_scheme.cols());
for (size_t vol = 0; vol != pos[3].size(); ++vol)
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