rordenlab/dcm2niix v1.0.20261029

version 29-October-2026 (v1.0.20261029)

on GitHub

Behaviour changes

• -ba y redacts the CMRR measurement UUID from WipMemBlock. -ba y is the default; use -ba o or -ba n to keep it.
• Siemens 2D AcquisitionTime. Reports the earliest slice of the first volume (the origin of SliceTiming), not instance 1; date-aware across midnight.
• Philips Dixon. Water/fat/in-phase/out-phase are separate series with _water/_fat/_inphase/_outphase postfixes and rec- entities in BidsGuess and %h/%H names.
• Parametric Maps. Multi-channel maps are split by LUTLabel into one file per channel. Validation Dataset.
• ASL RepetitionTime. ASL keeps the per-shot TR; the issue 1024 volume-TR override no longer applies to perfusion series.
• BIDS sidecars. Siemens partial Fourier emits PartialFourierDirection PHASE; TablePosition prints 0 not -0; NumberOfKSpaceTrajectories is MRS-only; UIH (0018,9082) is read as EffectiveEchoSpacing, not echo time, and BWPE as per acquired pixel (issue 1035).

New features

• Multi-delay pCASL. Siemens XA tgse_pcasl_loft is decoded to BIDS ASL (per-volume PostLabelingDelay, _aslcontext.tsv, dummy-volume removal via reproinx).
• CMRRMeasurementUUID in CMRR imaging and physio sidecars (-ba n only), pairing physio with image series.
• Series listing. -n -2 writes dcm2niix_series.json without converting; -n -1 no longer touches files (previously -n -1 -w 1 deleted existing outputs).
• Browser package @niivue/dcm2niix 1.4: convert(), listSeries(), groupOutputs(), exitCodes, shipped TypeScript declarations; one JPEG-LS/JPEG 2000 build (/plain and /jpeg are aliases); output names follow the input's shared top folder (loose files or several top-level folders still give input_); inputs are read lazily from the File (WORKERFS) with a read-ahead cache; WASM heap may grow to 4 GB and outputs are freed as collected.
• Filename specifiers %@ (station name) and %= (device serial number).
• BIDS classification. Siemens T1w spin echo and T1 SPACE; MP2RAGE RepetitionTimePreparation; dzne_ep3d ReadPolarity.
• ReproIn. Stricter entity/bareword parsing, ses-{date}, inv entity; reproinx run correspondence and stale B0Field link cleanup.

Fixes

• Malformed JPEG lossless, JPEG 2000 and JPEG-LS frames whose size disagrees with the DICOM header (including one codestream under a multi-frame header, or a mosaic split into frames) are rejected instead of over-reading memory or returning uninitialized pixels; TurboJPEG builds check the same; JPEG-LS and TurboJPEG no longer leak their input buffers.
• JPEG: lossless multi-frame images with several fragments per frame, Extended JPEG (.51) including 12-bit (issue 1054), and encapsulated multi-frame files decoded at their own item offsets.
• GE MR30 DWI: VascularCollapseFlag 3/4/5 gradients and per-volume trace detection; clearer missing-image messages report the image total ("expected 210 images (42 spatial positions per volume)") (thanks to PR #1056).
• Faster conversion: per-file parser setup no longer zeroes a 9 MB table (regression from the Parametric Map split), and Siemens ASCII protocol arrays (alTI, alTE, WipMemBlock alFree/adFree, free diffusion directions) are read in one pass instead of one full scan per index (XA studies 2.3× faster natively, ~25% in the browser).
• Compressed (JPEG-LS, JPEG 2000, RLE) enhanced DICOM keeps Dimension Index frame order and per-frame scaling; 4D JPEG lossless decodes all frames; RLE RGB planar configuration 1.
• Rename mode (-r y) fails closed on read/write errors; byte-identical inputs are skipped, true conflicts return exit 8.
• Stack overflows: macOS MRSI segfault (PR #1042) and Windows 32 MB stack reserve (issue 1040).
• CMake superbuild forwards toolchain, macOS SDK and architectures; Cloudflare zlib pinned; OpenJPEG flags preserved on non-MSVC; Windows wheel build.
• pigz hint shown only in verbose mode (issue 1027).