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MCX v2025 (Jumbo Jolt)

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@fangq fangq released this 14 Feb 03:14
v2025
0fa0605

Monte Carlo eXtreme (MCX) - CUDA Edition

v2025

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What's New

MCX v2025 is a maintenance release with multiple bug fixes and minor new features. It is highly
recommended to upgrade for all users.

Notable major bug fixes include

  • a high priority bug #222, introduced in 198cd34, was fixed. this bug affects all simulations
    since v2023. Particularly, when a photon has a long pathlength, with weight drops to numerical 0,
    its pathlength data is carried in the immediately launched new photon, causing skews in the
    detected photon pathlength distributions
  • further updates to the handling of low absorption medium (#164), previously affect not-so-low mua values
  • a bug fix related to multi-source simulation to properly return the source ID (#217)
  • fix angleinvcdf and invcdf in pmcx that was previously not enabled (#233)
  • fix svmc flipped normal direction only in mcxlab for Octave (#221)
  • fix continuous media nan handling (#224, #225)
  • fix the bug that prevents the use of photon-sharing with pattern3d source
  • correctly store detector ID and initial launch pixel index in pattern3d photon-sharing simulations
  • for all brain related simulations, we have updated the CSF mua value of 0.004/mm that was
    previously used in Custo et al. 2006 paper to 0.0004/mm, matching its upstream reference Strangman et al. 2003.
    However, we want to highlight that both literature may not provide the best mua value for CSF - as such low
    mua/mus CSF properties are mostly for CSF in the inner part of the brain, but not representiative to those in
    the subarachnoid space. A few literature have shown that CSF in the subarachnoid space may have a higher
    mus' value, in the range between 0.16/mm to 0.32/mm, as shown in Okada et al. 2003
  1. [Okada_2003]
    E. Okada and D. T. Delpy, "Near-infrared light propagation in an adult head model. I. Modeling of low-level scattering in the cerebrospinal fluid layer," Applied Optics 42, 2906–2914 (2003)
  2. [Custo_2006]
    A. Custo, W. M. Wells III., A. H. Barnett, et al., "Effective scattering coefficient of the cerebral spinal fluid in adult head models for diffuse optical imaging," Applied Optics 45, 4747 (2006)
  3. [Strangman_2003]
    G. Strangman, M. A. Franceschini, and D. A. Boas, "Factors affecting the accuracy of near-infrared spectroscopy concentration calculations for focal changes in oxygenation parameters," NeuroImage 18, 865–879 (2003)

In addition, in this release, we also added the following key new features

  • the new -N/--net command line flag allows one to browse and run growing number of community-contributed
    simulations hosted on https://neurojson.io (one can browse the list at https://neurojson.org/db/mcx)
  • mcx can read JSON input file from stdin (standard input) using pipe, allow one to use advanced text processing utilities in the shell,
    such as sed, perl, jq to modify JSON inputs at runtime. For example mcx -N cube60 --dumpjson | jq '.Forward.Dt=1e-10' | mcx -f
  • a new shortcut option -Q for --bench to conveniently browse and run built-in benchmarks
  • a new demo script demo_mcxlab_replay_traj.m to show how to use replay to produce trajectories between source/detector
  • mcxlab and pmcx cam set cfg.flog=1 or 0 to disable printing of mcx banner
  • setting a negative detector radius creates excluded detection areas, making it possible to create ring-shaped detectors

The detailed updates can be found in the below change log

  • 2025-01-22 [24b445e] [bug] fix incorrect per-voxel pathlength when mua->0, #164
  • 2025-01-21 [1f536ba] [bug] fix windows -N error
  • 2025-01-21 [aeca212] [cmake] update cmake to add -N support
  • 2025-01-21 [134ab82] [ci] fix windows msvc compilation error
  • 2025-01-21 [12071fd] [feat] add -N/--net to download simulations from NeuroJSON.io, add -Q
  • 2025-01-10 [cf10d5f] [pmcx] Parse issavedet field of the cfg dict as an int instead of a bool.
  • 2025-01-03 [8f433e9] [feat] allow plotting logical arrays in mcxplotvol
  • 2024-12-15 [eafea84] [feat] polish and miss_hit format of demo_mcxlab_replay_traj.m
  • 2024-12-15 [82e100b] [feat] add missing demo_mcxlab_replay_traj.m script
  • 2024-12-11 [22bf12a] [bug] fix mcxlab castlist
  • 2024-12-04 [86dcba9] [bug] force most scalar inputs to be double to avoid incorrect typecasting
  • 2024-11-25 [4b7020d] [ci] upgrade pmcx macos build to macos-13
  • 2024-11-25 [51e9970] [bug] fix mcx crash when replay is requested without seed file
  • 2024-11-22 [e8907db] [ci] include vcomp140.dll in windows binary
  • 2024-11-22 [2902119] [ci] further test vcomp140
  • 2024-11-22 [c3d413d] [ci] find vcomp140.dll
  • 2024-11-21 [4f1335c] [ci] print vcomp1xx.dll path
  • 2024-11-21 [d033755] [bug] apply patch in #235 to pmcx, bump pmcx to v0.3.6
  • 2024-11-21 [744c088] [bug] correctly return integer based w0 and detid in pattern3d
  • 2024-11-21 [dcf11c4] [bug] enable photon sharing for pattern3d source
  • 2024-11-18 [bd62362] [bug] fix mcxlab crash with >2^31-1 voxels, fix #235, revert #164
  • 2024-11-13 [188338b] [feat] negative detector radius captures but does not save photons
  • 2024-11-12 [dfc704f] [ci] reduce macos binary size using strip
  • 2024-11-12 [7d33c14] [ci] disable octave download on macos
  • 2024-11-12 [43e7416] [ci] download octave app with -L
  • 2024-11-12 [c978a3e] [ci] use octave app on macos
  • 2024-11-12 [30cc3cb] [ci] upload macos mcx package
  • 2024-11-12 [24d1257] [ci] downgrade download-artifact as it does not support multiple jobs
  • 2024-11-10 [f17dcc6] [bug] fix mcxlab crash when using issave2pt=0 with photonsharing
  • 2024-11-09 [8c69db3] [ci] update setup.py for pmcx
  • 2024-11-09 [fd83829] [ci] disable CMAKE_RANLIB
  • 2024-11-09 [dbada19] [ci] debug ranlib
  • 2024-11-09 [208c31d] [ci] use verbose option to debug macos build flags
  • 2024-11-09 [4e0c672] [bug] fix maskdet 1cube test
  • 2024-11-08 [ee5be15] [feat] make onecube benchmark maskdet work, fix --dumpmask
  • 2024-11-08 [f2d3bc4] [feat] support 1x1x1 volume, add onecube/twocube benchmarks, det not working
  • 2024-11-06 [eaafb0b] [feat] disabling issaveref if issave2pt is false
  • 2024-10-09 [0411ec6] Fix data ordering in traj.iquv
  • 2024-09-25 [8c0cfec] [pmcx] bump up pmcx version to 0.3.5 after fixing #233
  • 2024-09-25 [58dec12] [bug] angleinvcdf and invcdf are not read in full in pmcx, fix #233
  • 2024-09-14 [7b8ecb6] [ci] restore macos-12
  • 2024-09-13 [6fbf3db] [bug] fix the potential typo in Custo et al for CSF mua, fix #232
  • 2024-09-03 [c9456a7] [ci] fix action alert related to download-artifact
  • 2024-08-22 [70f95ba] [pmcx] fix CI error for pmcx
  • 2024-08-22 [82fb8f1] [feat] allow mcxlab and pmcx to use cfg.flog to control log printing
  • 2024-08-18 [17e347c] [bug] fix lzma memory leakage, NeuroJSON/zmat#11, lloyd/easylzma#4
  • 2024-08-06 [5cc92ab] [bug] avoid using the same RNG seed when -E -1 on multiple GPUs
  • 2024-08-06 [3c480b6] [doc] clarify the default RNG seed (1648335518) in html doc
  • 2024-07-22 [d8959eb] [ci] update macos-11 to 12 as 11 no longer works
  • 2024-07-14 [b17cb1a] [bug] mcxplotshapes patch by ChenJY-L to plot Box, close #227
  • 2024-07-14 [78716e4] [bug] avoid overwriting mua/mus when one is nan, fix #224, fix #225
  • 2024-07-04 [80b5794] [bug] read g and n when mua or mus=nan in asgn_float, close #225, close #224
  • 2024-06-22 [f959c71] [bug] store reflection position in trajectory
  • 2024-06-19 [4ff5b60] [bug] print large photon numbers without overflow
  • 2024-06-11 [d66a0a3] [test] sync test script between mcx and mcxcl after fangq/mcxcl#57
  • 2024-06-11 [1e7d0f1] [bug] reset replay.tof when tof exceeds tend, like fangq/mcxcl#57
  • 2024-06-07 [026eebf] [bug] ensure to clear shared mem buffer regardless of weight, #222
  • 2024-06-06 [b41c915] [bug] fix skewed nscat distribution, fix #222
  • 2024-06-05 [654dff1] [bug] fix outputtype error in json2mcx, reformat with miss_hit
  • 2024-06-05 [25b0268] [feat] export iquv in trajectory data when cfg.istrajstokes=1
  • 2024-05-18 [0a76d17] [bug] fix mcxsvmc flipped normal direction in octave, fix #221
  • 2024-05-18 [2f42524] [ci] downgrade matlab from v2024a to v2022a
  • 2024-05-14 [56aa355] [doc] update jsonlan and neurojson toolbox download links
  • 2024-04-25 [ea67ea9] [bug] avoid double-base64-encoding when -Z 2 is used, fix #219
  • 2024-03-28 [3b7e11c] [doc] fix incorrect default value for gscatter
  • 2024-03-25 [b4706ae] [release] update winget mcxstudio package
  • 2024-03-18 [2953735] [doc] add documentation on the srcid output in detp and traj
  • 2024-03-18 [94961f3] [bug] return source ID in multi-source simulation, fix #217
  • 2024-03-17 [3c3d755] [release] post v2024.2 release action, close #216
  • 2024-03-17 [7902a4e] [mcxcloud] update docker image to v2024.2
  • 2024-03-15 [08bfe11] [feat] support _ArrayData_ in Shapes volume input
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