From b791a3af8132a4d9ab8c81320f1ba46467e9d5cb Mon Sep 17 00:00:00 2001 From: Paul McCarthy Date: Mon, 11 Dec 2017 16:21:11 +1030 Subject: [PATCH 1/3] New command line option allowing user to extract specific data series by number. --- console/main_console.cpp | 10 ++++++++++ console/nii_dicom_batch.cpp | 14 ++++++++++++++ console/nii_dicom_batch.h | 3 +++ 3 files changed, 27 insertions(+) diff --git a/console/main_console.cpp b/console/main_console.cpp index 36080386..5f2ec828 100644 --- a/console/main_console.cpp +++ b/console/main_console.cpp @@ -89,6 +89,7 @@ void showHelp(const char * argv[], struct TDCMopts opts) { printf(" -h : show help\n"); printf(" -i : ignore derived, localizer and 2D images (y/n, default n)\n"); printf(" -m : merge 2D slices from same series regardless of study time, echo, coil, orientation, etc. (y/n, default n)\n"); + printf(" -n : only convert this series number - can be used up to %i times (default convert all)\n", MAX_NUM_SERIES); printf(" -o : output directory (omit to save to input folder)\n"); printf(" -p : Philips precise float (not display) scaling (y/n, default y)\n"); printf(" -s : single file mode, do not convert other images in folder (y/n, default n)\n"); @@ -279,6 +280,15 @@ int main(int argc, const char * argv[]) } else if ((argv[i][1] == 'o') && ((i+1) < argc)) { i++; strcpy(opts.outdir,argv[i]); + } else if ((argv[i][1] == 'n') && ((i+1) < argc)) { + if (opts.numSeries < MAX_NUM_SERIES) { + i++; + opts.seriesNumber[opts.numSeries] = atoi(argv[i]); + opts.numSeries += 1; + } + else { + printf("Warning: too many series specified, ignoring -n %s\n", argv[i]); + } } else printf(" Error: invalid option '%s %s'\n", argv[i], argv[i+1]);; lastCommandArg = i; diff --git a/console/nii_dicom_batch.cpp b/console/nii_dicom_batch.cpp index 9b2a7d38..170ba1f1 100644 --- a/console/nii_dicom_batch.cpp +++ b/console/nii_dicom_batch.cpp @@ -2470,6 +2470,18 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmLis imgM = nii_flipZ(imgM, &hdr0); sliceDir = abs(sliceDir); //change this, we have flipped the image so GE DTI bvecs no longer need to be flipped! } + // skip converting if user has specified one or more series, but has not specified this one + if (opts.numSeries > 0) { + int i = 0; + for (; i < opts.numSeries; i++) { + if (opts.seriesNumber[i] == dcmList[dcmSort[0].indx].seriesNum) { + break; + } + } + if (i == opts.numSeries) { + return EXIT_SUCCESS; + } + } //move before headerDcm2Nii2 checkSliceTiming(&dcmList[indx0], &dcmList[indx1]); //nii_SaveBIDS(pathoutname, dcmList[dcmSort[0].indx], opts, dti4D, &hdr0, nameList->str[dcmSort[0].indx]); nii_SaveBIDS(pathoutname, dcmList[dcmSort[0].indx], opts, &hdr0, nameList->str[dcmSort[0].indx]); @@ -3184,6 +3196,8 @@ void setDefaultOpts (struct TDCMopts *opts, const char * argv[]) { //either "set opts->isVerbose = false; #endif opts->isTiltCorrect = true; + opts->numSeries = 0; + memset(opts->seriesNumber, 0, sizeof(opts->seriesNumber)); strcpy(opts->filename,"%f_%p_%t_%s"); } // setDefaultOpts() diff --git a/console/nii_dicom_batch.h b/console/nii_dicom_batch.h index f9f0ba93..ced863e7 100644 --- a/console/nii_dicom_batch.h +++ b/console/nii_dicom_batch.h @@ -22,10 +22,13 @@ extern "C" { }; #endif +#define MAX_NUM_SERIES 16 + struct TDCMopts { bool isSave3D,isGz, isFlipY, isCreateBIDS, isSortDTIbyBVal, isAnonymizeBIDS, isOnlyBIDS, isCreateText, isIgnoreDerivedAnd2D, isPhilipsFloatNotDisplayScaling, isTiltCorrect, isRGBplanar, isOnlySingleFile, isForceStackSameSeries, isCrop; int isVerbose, compressFlag, gzLevel; //support for compressed data 0=none, char filename[512], outdir[512], indir[512], pigzname[512], optsname[512], indirParent[512], imageComments[24]; + long seriesNumber[MAX_NUM_SERIES], numSeries; #ifdef HAVE_R bool isScanOnly; void *imageList; From 884007fffce5f7929434e93ed15bbd947c4a049b Mon Sep 17 00:00:00 2001 From: Paul McCarthy Date: Mon, 11 Dec 2017 16:21:48 +1030 Subject: [PATCH 2/3] Typo --- VERSIONS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSIONS.md b/VERSIONS.md index e70140ee..91d328b3 100644 --- a/VERSIONS.md +++ b/VERSIONS.md @@ -1,6 +1,6 @@ ## Versions -4-Dev-2017 +4-Dec-2017 - Handle implicit VR DICOMs where [critical values nested in sequence groups (SQ)](https://github.com/rordenlab/dcm2niix/commit/7f5649c6fe6ed366d07776aa54397b50f6641aff) - Better support for [PAR/REC files with segmented 3D EPI](https://github.com/rordenlab/dcm2niix/commit/66cdf2dcc60d55a6ef37f5a6db8d500d3eeb7c88). - Allow Protocol Name to be [empty](https://github.com/rordenlab/dcm2niix/commit/94f3129898ba83bf310c9ff28e994f29feb13068). From fa57f64cefe6340ac82979df11892e068323ff78 Mon Sep 17 00:00:00 2001 From: Paul McCarthy Date: Mon, 11 Dec 2017 16:29:40 +1030 Subject: [PATCH 3/3] Typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index f80a9fdc..6b768bf9 100644 --- a/README.md +++ b/README.md @@ -70,7 +70,7 @@ If you have any problems with the cmake build script described above or want to - [dcm2niir](https://github.com/muschellij2/dcm2niir) R wrapper for dcm2niix/dcm2nii. - [divest](https://github.com/jonclayden/divest) R interface to dcm2niix. - [sci-tran dcm2niix](https://github.com/scitran-apps/dcm2niix) docker. - - [neuro_docker](https://github.com/Neurita/neuro_docker) includes dcm2niix as part of a provides a single, static Dockerfile. + - [neuro_docker](https://github.com/Neurita/neuro_docker) includes dcm2niix as part of a single, static Dockerfile. - [neurodocker](https://github.com/kaczmarj/neurodocker) generates [custom](https://github.com/rordenlab/dcm2niix/issues/138) Dockerfiles given specific versions of neuroimaging software. - [dcm2niix_afni](https://afni.nimh.nih.gov/pub/dist/doc/program_help/dcm2niix_afni.html) is a version of dcm2niix included with the [AFNI](https://afni.nimh.nih.gov/) distribution. - [MRIcroGL](https://github.com/neurolabusc/MRIcroGL) is available for MacOS, Linux and Windows and provides a graphical interface for dcm2niix. You can get compiled copies from the [MRIcroGL NITRC web site](https://www.nitrc.org/projects/mricrogl/). \ No newline at end of file