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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 | ||
| ``` | ||
| 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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