From 9c446e05dd6056da1ef4cd07dd4f5d6dd14afa9c Mon Sep 17 00:00:00 2001 From: Qianqian Fang Date: Thu, 23 Jan 2025 17:18:06 -0500 Subject: [PATCH] [doc] update README.txt for v2025 updates --- README.txt | 38 +++++++++++++++++++++++++++++++++++++- 1 file changed, 37 insertions(+), 1 deletion(-) diff --git a/README.txt b/README.txt index e3b32475..b53f411c 100644 --- a/README.txt +++ b/README.txt @@ -18,7 +18,43 @@ Table of Content: == # What's New == -MCX v2025 main features. +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 + +* [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) +* [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) +* [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 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 | 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