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* commit 'v1.0.20171017-3-g9ccc4c0': Detect SMS using 0051,1011 if MosaicRefAcqTimes missing rordenlab#141 Hide NIfTI sliceOrder if protocolSliceNumber1 > 1 SliceTiming for reversed image numbering https://github.com/neurolabusc/dcm2niix/issues/40 Update dcm_qa submodule. New version (v1.0.20171017) Added link rordenlab#138 Store mulbiband factor in NIfTI descrip field (e.g. "mb=2") https://www.nitrc.org/forum/message.php?msg_id=22593 Add patient sex, weight, etc, https://www.nitrc.org/forum/message.php?msg_id=22567 Add ImageOrientationPatientDICOM and InPlanePhaseEncodingDirectionDICOM for 3D undistortion Compiling with CentOS 7: rordenlab#137 BIDS 1.0.2 DelayTime field for sparse fMRI Add InstitutionalDepartmentName Get ProtocolName from CSA header if it is not in DICOM header nipy/heudiconv#80 Change name of output tag of two variables to match DICOM Group PixelBandwidth with DwellTime in output json Vanquish compiler warnings. Report lower order shims prior to higher order (requested by mharms) Handle Siemens product gradient offsets? More Siemens information saved to BIDS BIDS: Do not set multiband factor for 3D EPI, report as "MRAcquisitionType": "3D",
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| Original file line number | Diff line number | Diff line change |
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| **Optional batch processing version:** | ||
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| Perform a batch conversion of multiple dicoms using the configurations specified in a yaml file. | ||
| ```bash | ||
| dcm2niibatch batch_config.yml | ||
| ``` | ||
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| The configuration file should be in yaml format as shown in example `batch_config.yaml` | ||
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| ```yaml | ||
| Options: | ||
| isGz: false | ||
| isFlipY: false | ||
| isVerbose: false | ||
| isCreateBIDS: false | ||
| isOnlySingleFile: false | ||
| Files: | ||
| - | ||
| in_dir: /path/to/first/folder | ||
| out_dir: /path/to/output/folder | ||
| filename: dcemri | ||
| - | ||
| in_dir: /path/to/second/folder | ||
| out_dir: /path/to/output/folder | ||
| filename: fa3 | ||
| ``` | ||
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| You can add as many files as you want to convert as long as this structure stays consistent. Note that a dash must separate each file. |
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| ## Versions | ||
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| 17-Oct-2017 | ||
| - Swap [phase-encoding direction polarity](https://github.com/rordenlab/dcm2niix/issues/125) for Siemens images where PE is in the Column direction. | ||
| - Sort diffusion volumes by [B-value amplitude](https://www.nitrc.org/forum/forum.php?thread_id=8396&forum_id=4703) (use "-d n"/"-d y" to turn the feature off/on). | ||
| - BIDS tag [TotalReadoutTime](https://github.com/rordenlab/dcm2niix/issues/130) handles partial fourier, Phase Resolution, etc (Michael Harms). | ||
| - Additional [json fields](https://github.com/rordenlab/dcm2niix/issues/127). | ||
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| 18-Aug-2017 | ||
| - Better BVec extraction for [PAR/REC 4.1](https://www.nitrc.org/forum/forum.php?thread_id=8387&forum_id=4703). | ||
| - Support for [Segami Cerescan volumes](https://www.nitrc.org/forum/forum.php?thread_id=8076&forum_id=4703). | ||
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| 24-July-2017 | ||
| - Compiles with recent releases of [OpenJPEG](https://github.com/neurolabusc/dcm_qa/issues/5#issuecomment-317443179) for JPEG2000 support. | ||
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| 23-June-2017 | ||
| - [Ensure slice timing always reported for Siemens EPI](https://github.com/neurolabusc/dcm_qa/issues/4#issuecomment-310707906) | ||
| - [Integrates validation](https://github.com/neurolabusc/dcm_qa) | ||
| - JSON fix (InstitutionName -> InstitutionAddress) | ||
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| 21-June-2017 | ||
| - Read DICOM header in 1Mb segments rather than loading whole file : reduces ram usage and [faster for systems with slow io](https://github.com/rordenlab/dcm2niix/issues/104). | ||
| - Report [TotalReadoutTime](https://github.com/rordenlab/dcm2niix/issues/98). | ||
| - Fix JPEG2000 support in [Superbuild](https://github.com/rordenlab/dcm2niix/issues/105). | ||
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| 28-May-2017 | ||
| - Remove all derived images from [Philips DTI series](http://www.nitrc.org/forum/message.php?msg_id=21025). | ||
| - Provide some [Siemens EPI sequence details](https://github.com/rordenlab/dcm2niix/issues). | ||
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| 28-April-2017 | ||
| - Experimental [ECAT support](https://github.com/rordenlab/dcm2niix/issues/95). | ||
| - Updated cmake to make JPEG2000 support easier with improved Travis and AppVeyor support [Ningfei Li](https://github.com/ningfei). | ||
| - Supports Data/Time for images that report Data/Time (0008,002A) but not separate Date and Time (0008,0022 and 0008,0032). | ||
| - [BIDS reports SliceTiming correctly](http://www.nitrc.org/forum/message.php?msg_id=20852). | ||
| - Options -1..-9 to control [gz compression level](https://github.com/rordenlab/dcm2niix/issues/90). | ||
| - Includes some [PET details in the BIDS JSON sidecar](https://github.com/rordenlab/dcm2niix/issues/87). | ||
| - Better detection of image order for Philips 4D DICOM (reported by Jason McMorrow and Stephen Wilson). | ||
| - [Include StudyInstanceUID and SeriesInstanceUID in filename](https://github.com/rordenlab/dcm2niix/issues/94). | ||
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| 7-Feb-2017 | ||
| - Can be compiled to use either Philips [Float or Display](http://www.nitrc.org/forum/message.php?msg_id=20213) intensity intercept and slope values. | ||
| - Handle 3D Philips DICOM and [PAR/REC](https://www.nitrc.org/forum/forum.php?thread_id=7707&forum_id=4703) files where images are not stored in a spatially contiguous order. | ||
| - Handle DICOM violations where icon is uncompressed but image data is compressed. | ||
| - Best guess matrix for 2D slices (similar to dcm2nii, SPM and MRIconvert). | ||
| - Linux (case sensitive filenames) now handles par/rec as well as PAR/REC. | ||
| - Images with unknown phase encoding do not generate [BIDS entry](https://github.com/rordenlab/dcm2niix/issues/79). | ||
| - Unified printMessage/printWarning/printError aids embedding in other projects, such as [divest](https://github.com/jonclayden/divest). | ||
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| 1-Nov-2016 | ||
| - AppVeyor Support (Ningfei Li & Chris Filo Gorgolewski) | ||
| - Swap 3rd/4th dimensions for GE sequential multi-phase acquisitions (Niels Janssen). | ||
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| 10-Oct-2016 | ||
| - Restores/improves building for the Windows operating system using MinGW. | ||
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| 30-Sept-2016 | ||
| - Save ImageType (0x0008,0x0008) to BIDS. | ||
| - Separate CT scans with different exposures. | ||
| - Fixed issues where some compilers would generate erratic filenames for zero-padded series (e.g. "-f %3s"). | ||
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| 21-Sept-2016 | ||
| - Reduce verbosity (reduce number of repeated warnings, less scary warnings for derived rather than raw images). | ||
| - Re-enable custom output directory "-o" option broken by 30-Apr-2016 version. | ||
| - Deal with mis-behaved GE CT images where slice direction across images is not consistent. | ||
| - Add new BIDS fields (field strength, manufacturer, etc). | ||
| - Philips PAR/REC conversion now reports inconsistent requested vs measured TR (due to prospect. motion corr.?). | ||
| - GE: Locations In Acquisition (0054, 0081) is inaccurate if slices are interpolated, use Images In Acquisition (0020,1002) if available. | ||
| - New filename options %d Series description (0008,103E), %z Sequence Name (0018,0024). | ||
| - New filename options %a antenna (coil) number, %e echo number. | ||
| - Initialize unused portions of NIfTI header to zero so multiple runs always produce identical results. | ||
| - Supports 3D lossless JPEG saved as [multiple fragments](http://www.nitrc.org/forum/forum.php?thread_id=5872&forum_id=4703). | ||
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| 5-May-2016 | ||
| - Crop 3D T1 acquisitions (e.g. ./dcm2niix -x y ~/DICOM). | ||
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| 30-Apr-2016 | ||
| - Convert multiple files/folders with single command line invocation (e.g. ./dcm2niix -b y ~/tst ~/tst2). | ||
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| 22-Apr-2016 | ||
| - Detect Siemens Phase maps (phase image names end with "_ph"). | ||
| - Use current working directory if file name not specified. | ||
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| 12-Apr-2016 | ||
| - Provide override (command line option "-m y") to stack images of the same series even if they differ in study date/time, echo/coil number, or slice orientation. This mechanism allows users to concatenate images that break strict DICOM compliance. | ||
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| 22-Mar-2016 | ||
| - Experimental support for [DICOM datasets without DICOM file meta information](http://dicom.nema.org/dicom/2013/output/chtml/part10/chapter_7.html). | ||
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| 12-Dec-2015 | ||
| - Support PAR/REC FP values when possible (see PMC3998685). | ||
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| 11-Nov-2015 | ||
| - Minor refinements. | ||
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| 12-June-2015 | ||
| - Uses less memory (helpful for large datasets). | ||
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| 2-Feb-2015 | ||
| - Support for Visual Studio. | ||
| - Remove dependency on zlib (now uses miniz). | ||
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| 1-Jan-2015 | ||
| - Images separated based on TE (fieldmaps). | ||
| - Support for JPEG2000 using OpenJPEG or Jasper libraries. | ||
| - Support for JPEG using NanoJPEG library. | ||
| - Support for lossless JPEG using custom library. | ||
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| 24-Nov-2014 | ||
| - Support for CT scans with gantry tilt and varying distance between slices. | ||
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| 11-Oct-2014 | ||
| - Initial public release. |
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