From 7d62584d68524587b11fe52648489c19edd752ee Mon Sep 17 00:00:00 2001 From: neurolabusc <rorden@sc.edu> Date: Tue, 30 Jul 2024 10:17:22 -0700 Subject: [PATCH] Bruker kludge (https://github.com/rordenlab/dcm2niix/issues/839) --- console/nii_dicom.cpp | 63 +++++++++++++++++++++++++++++++++++++++++++ console/nii_dicom.h | 2 +- 2 files changed, 64 insertions(+), 1 deletion(-) diff --git a/console/nii_dicom.cpp b/console/nii_dicom.cpp index 46dad9bf..680316e2 100644 --- a/console/nii_dicom.cpp +++ b/console/nii_dicom.cpp @@ -4717,6 +4717,10 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD int locationsInAcquisitionGE = 0; int PETImageIndex = 0; int inStackPositionNumber = 0; + int isIssue839 = false; + float patientPosition1[kMaxSlice2D]; + float patientPosition2[kMaxSlice2D]; + float patientPosition3[kMaxSlice2D]; bool isKludgeIssue533 = false; uint32_t dimensionIndexPointer[MAX_NUMBER_OF_DIMENSIONS]; size_t dimensionIndexPointerCounter = 0; @@ -4930,10 +4934,24 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD acquisitionTimePhilips = - 1.0; } int ndim = nDimIndxVal; + //issue 839 + patientPosition1[numDimensionIndexValues] = patientPosition[1]; + patientPosition2[numDimensionIndexValues] = patientPosition[2]; + patientPosition3[numDimensionIndexValues] = patientPosition[3]; if (inStackPositionNumber > 0) { //for images without SliceNumberMrPhilips (2001,100A) int sliceNumber = inStackPositionNumber; //printf("slice %d \n", sliceNumber); + if ((!isIssue839) && (sliceNumber == 1) && (!isnan(patientPositionStartPhilips[1]))) { + float dx = sqrt( + pow(patientPositionStartPhilips[1] - patientPosition[1], 2) + + pow(patientPositionStartPhilips[2] - patientPosition[2], 2) + + pow(patientPositionStartPhilips[3] - patientPosition[3], 2)); + if (!isSameFloatGE(dx, 0.0)) { + isIssue839 = true; + printWarning("repeats of first inStackPositionNumber are at different locations (dx = %gmm; issue 839)\n", dx); + } + } if ((sliceNumber == 1) && (!isnan(patientPosition[1]))) { for (int k = 0; k < 4; k++) patientPositionStartPhilips[k] = patientPosition[k]; @@ -7901,6 +7919,51 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD // printWarning("3D EPI with FrameAcquisitionDuration = %gs volumes = %d (see issue 369)\n", frameAcquisitionDuration/1000.0, d.xyzDim[4]); if (numDimensionIndexValues > 1) strcpy(d.imageType, imageType1st); //for multi-frame datasets, return name of book, not name of last chapter + if (((d.isValid)) && (isIssue839) && (numDimensionIndexValues > 2)) { + //rewrite + for (int j = 0; j < MAX_NUMBER_OF_DIMENSIONS; j++) { + for (int i = 0; i < numDimensionIndexValues; i++) { + dcmDim[i].dimIdx[j] = 0; + } + } + // we need a scalar value for sorting + // first pass: find slice that is furthest from isocenter, n.b. arbitrary if tied + float mxDx = 0.0; + int mxIdx = 0; // + for (int i = 0; i < numDimensionIndexValues; i++) { + float dx = sqrt(pow(patientPosition1[i],2)+pow(patientPosition2[i],2)+pow(patientPosition3[i],2)); + if (dx > mxDx) { + mxDx = dx; + mxIdx = i; + } + if (isVerbose > 1) printf("slice %d is %gmm from isocenter\n", i, dx); + } + if (isVerbose > 1) printf("slice %d is furthest (%gmm) from isocenter\n", mxIdx, mxDx); + // second pass: measure each slices scalar distance from furthest slice + // ensure their are no repeated slice positions + fidx *objects = (fidx *)malloc(sizeof(struct fidx) * numDimensionIndexValues); + bool isSamePosition = false; + for (int i = 0; i < numDimensionIndexValues; i++) { + float dx = sqrt(pow(patientPosition1[i]-patientPosition1[mxIdx],2)+pow(patientPosition2[i]-patientPosition2[mxIdx],2)+pow(patientPosition3[i]-patientPosition3[mxIdx],2)); + if (isVerbose > 1) printf("slice %d is %gmm from furthest slice\n", i, dx); + objects[i].value = dx; + //sliceMM[i]; + objects[i].index = i; + if ((i != mxIdx) && (isSameFloatGE(dx, 0.0))) + isSamePosition = true; + } + if (isSamePosition) { + printError("Multivolume file with invalid DimensionIndexValues (issue839)\n"); + d.isValid = false; + } + qsort(objects, numberOfFrames, sizeof(struct fidx), fcmp); + numDimensionIndexValues = numberOfFrames; + for (int i = 0; i < numDimensionIndexValues; i++) { + dcmDim[objects[i].index].dimIdx[0] = i; + } + d.xyzDim[4] = 1; + d.xyzDim[3] = numDimensionIndexValues; + } //issue839 if ((numDimensionIndexValues > 1) && (numDimensionIndexValues == numberOfFrames)) { //Philips enhanced datasets can have custom slice orders and pack images with different TE, Phase/Magnitude/Etc. int maxVariableItem = 0; diff --git a/console/nii_dicom.h b/console/nii_dicom.h index 39200ef0..e8f2b07a 100644 --- a/console/nii_dicom.h +++ b/console/nii_dicom.h @@ -50,7 +50,7 @@ extern "C" { #define kCPUsuf " " //unknown CPU #endif -#define kDCMdate "v1.0.20240327" +#define kDCMdate "v1.0.20240730" #define kDCMvers kDCMdate " " kJP2suf kLSsuf kCCsuf kCPUsuf static const int kMaxEPI3D = 1024; //maximum number of EPI images in Siemens Mosaic