""
"▵"
"To expand or collapse the command window."
"▾"
"Load seed data from previous simulations for replay"
"Send"
""
"Clear Output"
"MCX Studio"
"Let MCX decide thread/block size (-A)"
""
"DebugFlags"
""
"Run remote command:"
""
"Replay"
""
"Lock GPU"
""
"Do normalization (-U)"
""
"Do reflection all boundaries (-b)"
""
"Save fluence (-S)"
""
"Save detected photons (-d)"
""
"Save volume mask (-M)"
""
"Save diffuse reflectance (-X)"
""
"Save photon seeds (-q)"
""
"Shared file system"
""
"Show progress bar"
""
"Skip void space (-k)"
""
"Do specular reflection (-V)"
""
"Orign from [0,0,0] (-z)"
""
""
""
"64"
"BubbleSize"
"-2"
""
""
""
"10000000"
"GateNum"
""
""
""
""
""
"1e6"
"Integer"
""
"Built-in ssh"
"ReplayDet"
""
""
"1648335518"
"A large integer or .mch file name"
""
""
"16384"
""
"1"
""
"100"
"Comma separated numbers"
"Advanced Settings"
""
""
"Basic Settings"
"Boundary cond."
"Save detected photon"
"GPU Settings"
"Run Monte Carlo simulation with"
""
"Switches"
"About MCX"
"Thread number (-t)"
"-t (--thread)"
"or"
"-a (--array)"
"Output format"
"-u (--unitinmm)"
"Run MCX on"
"-G (--gpu)"
"Seed (-E)"
"-E (--seed)"
"Output type (-O)"
"-O (--outputtype)"
"Workload split"
"-W (--workload)"
"Debug flags"
"-D (--debuglevel)"
"Replay detector ID (-Y)"
"-Y (--replaydet)"
"Additional parameters"
"-Y (--replaydet)"
"or"
"-a (--array)"
"Thread block size (-T)"
"-T (--blocksize)"
"Total photon number (-n)"
"-n (--photon)"
"Session ID (-s)"
"-s (--sessionid)"
"User Input>"
"Array order (-a)"
"-a (--array)"
"Gate group size (-g)"
"-g (--gategroup)"
"Voxel size in mm (-u)"
"-u (--unitinmm)"
"Max detected photons(-H)"
"-H (--maxdetphoton)"
"Atomic operations"
"(--atomic)"
"Cache radius from src (-R)"
"-r (--skipradius)"
"Repetition (-r)"
"-r (--repeat)"
"Session"
"DoSave"
"DoNormalize"
"Autopilot"
"SaveDetector"
"DetectedNum"
"GPUID"
"UnitInMM"
"DoSaveRef"
"DoSaveSeed"
"DoSkipVoid"
"InputFile"
"DoSrcFrom0"
"MediaCfg"
"DetectorCfg"
"MCXConfig"
"Workload"
"ShapeCfg"
"Seed"
"DoSaveMask"
"DebugFlags"
"ReplayDet"
"ThreadNum"
"DoReplay"
"MCProgram"
"DoSpecular"
"UseAtomic"
"BasicOrder"
"DebugPhoton"
"MoreParam"
"RemoteCmd"
"DoRemote"
"DoSharedFS"
"ThreadBlock"
"OutputFormat"
"OutputType"
"Boundary"
"SaveDetFlag"
"Benchmark"
"PhotonNum"
"RespinNum"
"ArrayOrder"
"BubbleSize"
"GateNum"
"DoReflect"
"About"
"About the author"
"New"
"Add a new task"
"Setting"
"Modify default paths"
"Copy session to clipboard"
"Default"
"Set default values"
"Delete"
"Delete selected task"
"Download volume labels (*_vol.nii)"
"_vol.nii"
"Download fluence"
"Download detected photon data (*.mch)"
".mch"
"Exit"
"Exit MCX Studio"
"Help"
"Browse help information"
"Options"
"List command line options"
"Open"
"Open a project or volume file"
"Paste session from clipboard"
"Plot fluence (jnii)"
".jnii"
"Plot fluence (mc2)"
".mc2"
"Plot mesh"
"Plot fluence (nii)"
".nii"
"Plot Volume"
"_vol.nii"
"GPU"
"List GPU Info"
"Run"
"Run selected task"
"Run All"
"Run all tasks"
"Save"
"Save tasks to a project file"
"Stop"
"Terminate current task"
"Toggle View"
"Verify"
"Verify parameters"
"Web"
"MCX homepage"
"mcxSetCurrent"
"File"
"Settings"
"Run"
"Open output folder"
"Plot volume (_vol.nii)"
"Download fluence (mc2/nii/hdr/img)"
"Tools"
"Download detected photon data (mch)"
"Download volume mask (_vol.nii)"
"MCX Documentation"
"http://mcx.space/wiki/?Learn#mcx"
"MMC Documentation"
"http://mcx.space/wiki/?Learn#mmc"
"MCX-CL Documentation"
"http://mcx.space/wiki/?Learn#mcxcl"
"MCX/MCXCL User Forum (mcx-users)"
"https://groups.google.com/forum/?hl=en#!forum/mcx-users"
"Help"
"MMC User Forum (mmc-users)"
"https://groups.google.com/forum/?hl=en#!forum/mmc-users"
"Iso2Mesh User Forum (iso2mesh-users)"
"https://groups.google.com/forum/?hl=en#!forum/iso2mesh-users"
"Download Nightly-Build"
"http://mcx.space/nightly/"
"MCX Github"
"https://github.com/fangq/mcx"
"MMC Github"
"https://github.com/fangq/mmc"
"MCX-CL Github"
"https://github.com/fangq/mcxcl"
"Report MCX Issues"
"https://github.com/fangq/mcx/issues"
"Report MMC Issues"
"https://github.com/fangq/mmc/issues"
"Report MCX-CL Issues"
"https://github.com/fangq/mcxcl/issues"
"MCX GPU Speed Benchmark Database"
"http://mcx.space/gpubench/"
"Refereces"
"[Fang2009] Original MCX Paper"
"http://www.osapublishing.org/oe/abstract.cfm?uri=oe-17-22-20178"
"[Fang2010] Original MMC Paper"
"https://www.osapublishing.org/boe/abstract.cfm?uri=boe-1-1-165"
"[Yu2018] Original MCX-CL Paper"
"https://www.spiedigitallibrary.org/journals/journal-of-biomedical-optics/volume-23/issue-01/010504/Scalable-and-massively-parallel-Monte-Carlo-photon-transport-simulations-for/10.1117/1.JBO.23.1.010504.full?SSO=1#ArticleLink"
"[Fang2011] MMC ray-tracing comparison"
"https://www.osapublishing.org/boe/abstract.cfm?uri=boe-2-5-1258"
"[Fang2012] SIMD MMC"
"https://www.osapublishing.org/boe/abstract.cfm?uri=boe-3-12-3223"
"[Yao2016] Widefield MMC"
"https://www.osapublishing.org/boe/abstract.cfm?uri=boe-7-1-171"
"[Yao2018] Jacobians with photon replay"
"https://www.osapublishing.org/boe/abstract.cfm?uri=boe-9-10-4588"
"[Yan2019] Dual-grid MMC"
"https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1117%2F1.JBO.24.2.020503&data=02%7C01%7Cq.fang%40northeastern.edu%7Cbb8daa56735543068b9c08d697592492%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636862806460866013&sdata=2dWyN3eVPwwymydjXEWIHBfVZI43Fcl5zuZ8wiaJ10k%3D&reserved=0"
"MCX Main Web"
"Table of all input flags"
"http://bit.ly/2K0rG4R "
"[Fang2019] GPU MMC"
"http://dx.doi.org/10.1117/1.JBO.24.11.115002"
"[Brain2Mesh2020] Brain2Mesh brain meshing toolbox"
"https://doi.org/10.1117/1.NPh.7.1.015008"
"[Yuan2020] PBM over lifespan"
"https://doi.org/10.1117/1.NPh.7.1.015009"
"[Yuan2021] Implicit MMC (iMMC)"
"https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-12-1-147"
"[Yan2020] SVMC hybrid method"
"https://www.osapublishing.org/boe/abstract.cfm?uri=boe-11-11-6262"
"Open Volume Viewer"
"Volume Designer"
"Clear Log"
"Copy selected"
"Export self-contained JSON input file"
"Print MATLAB plotting commands only"
"Open Photon History File (*.mch)"
"Open existing project"
"Open Photon History File (*.mch)"
"Built-in"
"User-defined »"
"Use Input File (-f)"
"Save project as"
"Status: idle"
"Value"
""
""
"μa (1/mm)"
"μs (1/mm)"
"g (anisotropy)"
"n (reflective index)"
""
"Box"
"Add a 3D box (using the center of the voxels - i.e. add 0.5 in all directions)"
"Cylinder"
"Add a cylinder"
"Grid"
"Define a uniform grid as the simulation space"
"Name"
"Define a name for the domain"
"Origin"
"Define the origin for subsequent objects"
"Sphere"
"Add a 3D sphere"
"Subgrid"
"Add a 3D box (using the lower-corner of the voxel)"
"Upper"
"Add an upper-space defined by a linear inequality"
"XLayers"
"Add a layered structure along x-axis"
"XSlabs"
"Add a slab along x-axis"
"YLayers"
"Add a layered structure along y-axis"
"YSlabs"
"Add a slab along y-axis"
"ZLayers"
"Add a layered structure along z-axis"
"ZSlabs"
"Add a slab along z-axis"
"Delete"
"Delete selected object"
"Edit"
"Preview"
"Preview"
"Print"
"Print selected object"
"Reset"
"Reset to a 60x60x60 homogeneous cubic domain"
"Additional Settings"
"Media Settings"
"Detector Settings (in voxel unit)"
"Simulation Designer"
"Volume Designer"
"Validate"
"MCX Ribon"
"ToolBar2"
"ToolBar3"
"Plot ▾"
"Plot MCX output data"
"ToolButton12"
"ToolButton13"
"ToolButton17"
"ToolButton35"
"Reset volume and define a different dimension"
"ToolButton5"
"Reset"
"ToolButton8"
"Help ▾"
"Browse help information"
"ShapeCfg"
""