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bvec signs for GE DTI with Coronol + ROW (#970) #971

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Merged
neurolabusc merged 1 commit into from
Sep 2, 2025
Merged

bvec signs for GE DTI with Coronol + ROW (#970) #971

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2 changes: 1 addition & 1 deletion console/nii_dicom.h
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ extern "C" {
#define kCPUsuf " " // unknown CPU
#endif

#define kDCMdate "v1.0.20250626"
#define kDCMdate "v1.0.20250827"
#define kDCMvers kDCMdate " " kJP2suf kTurbosuf kLSsuf kCCsuf kCPUsuf

static const int kMaxEPI3D = 1024; // maximum number of EPI images in Siemens Mosaic
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19 changes: 13 additions & 6 deletions console/nii_dicom_batch.cpp
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Expand Up @@ -303,6 +303,12 @@ void geCorrectBvecs(struct TDICOMdata *d, int sliceDir, struct TDTI *vx, int isV
if (abs(sliceDir) != 3)
printWarning("Limited validation for non-Axial DTI: confirm gradient vector transformation.\n");
// GE vectors from Xiangrui Li' dicm2nii, validated with datasets from https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging
//
// GE → FSL bvec (see issue 970) for unit vector
// 1) Apply plane-dependent flip first
// 2) Always negate Y
// 3) ROW swap/flip (if !col)
// 4) Negate all components (compatibility)
ivec3 flp;
if (abs(sliceDir) == 1)
flp = setiVec3(1, 1, 0); // SAGITTAL
Expand Down Expand Up @@ -353,18 +359,19 @@ void geCorrectBvecs(struct TDICOMdata *d, int sliceDir, struct TDTI *vx, int isV
vx[i].V[2] = vx[i].V[2] * bVecScale;
vx[i].V[3] = vx[i].V[3] * bVecScale;
}
for (int v = 0; v < 3; v++)
if (flp.v[v] == 1)
vx[i].V[v + 1] = -vx[i].V[v + 1];
vx[i].V[2] = -vx[i].V[2]; // we read out Y-direction opposite order as dicm2nii, see also opts.isFlipY
// 3) ROW swap/flip (if !col) (see issue 970)
if (!col) { // rows need to be swizzled
// see Stanford dataset Ax_DWI_Tetrahedral_7 unable to resolve between possible solutions
// http://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging
float swap = vx[i].V[1];
vx[i].V[1] = vx[i].V[2];
vx[i].V[2] = swap;
vx[i].V[2] = -vx[i].V[2]; // because of transpose?
}
for (int v = 0; v < 3; v++)
if (flp.v[v] == 1)
vx[i].V[v + 1] = -vx[i].V[v + 1];
vx[i].V[2] = -vx[i].V[2]; // we read out Y-direction opposite order as dicm2nii, see also opts.isFlipY
vx[i].V[1] = -vx[i].V[1]; // because of transpose?
}
}
// These next lines are only so files appear identical to old versions of dcm2niix:
// dicm2nii and dcm2niix generate polar opposite gradient directions.
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