records/reference.json

{
 "body_sha256": "49f932d4c234baf0a869aa614b963990e6538dd1a59f3f41d75e7e3e4620a0f6",
 "caveats": {
  "echo_spacing": "Only their te = 100 us train is reproduced: it is the one their relaxivities were fitted on. The te-DEPENDENCE of their trains (100 us to 20 ms) IS the garnet's internal-gradient effect, and a label-volume pack carries no C3 field channel, so a longer-te train is refused by name rather than served as a decay without its dephasing.",
  "grade": "The pre-protocol record of this family stated grade B as a FIELD, reasoning that the paper prints no T2 value. grade_of assigns A by rule: the quantity is read from their own RELEASED echo trains, which ARE the measurement, on the same physical object. What the absence of a printed number costs is the reference's uncertainty -- it is 0.0 with a reason, so the `published-` comparison cannot be failed on and its disagreement is recorded instead.",
  "mixtures": "The three MIXTURES have no reference row. LabelVolume accumulates ONE boundary local time over every wall and Tissue.rho is one scalar, so a single pack cannot carry Ling's 12.5 um/s on quartz and 98.5 um/s on garnet at once. They are built, certified, gated and published -- the geometry, the positions and the contact channel are all sound -- and their spec declares NO nominal relaxivity, so a consumer must state one. Recorded as blocked (dmipy-sim#491), not approximated with one of the two numbers.",
  "windows": "The five packs do not share a window: 3.5 s for the two quartz-rich packs (35,000 echoes) and 2.0 s for the three garnet-rich ones (20,000 echoes), each the extent of ITS OWN released train. The design's window is the longest and each pack's own is in the walk record."
 },
 "crossref": {
  "agency": "crossref",
  "container": "Transport in Porous Media",
  "doi": "10.1007/s11242-022-01764-w",
  "resolved": "2026-09-27T01:17:40Z",
  "title": "Model Synthetic Samples for Validation of NMR Signal Simulations",
  "type": "journal-article"
 },
 "description": "Resin-set quartz and garnet sand packs whose CPMG was measured and whose pore space was then imaged: the relaxometry reference where the measurement and the geometry are the SAME object. Relaxation is not in the walk, so one pack answers every relaxivity.",
 "doi": "10.1007/s11242-022-01764-w",
 "geometry_derivation": "the geometry is the released one when no free parameter marked 'ours' changes it; none of this family's parameters does",
 "geometry_parameters_ours": [],
 "inputs_sha256": "441526872b5bd57169d88f18d0974666682d06d84acc8d34502e1362bc3bd174",
 "licence_note": "CC-BY-4.0 images and echo trains; the packs are CC-BY-4.0 and no byte of the deposit is redistributed",
 "parameters": [
  {
   "changes_geometry": false,
   "how": "fitted by them per mineral to their own te = 100 us trains; an effective value tied to their 3.93 um voxel, because a segmentation's surface is the Manhattan area at that resolution, which is what both walks relax against",
   "name": "rho",
   "unit": "m/s",
   "value": {
    "garnet": 9.85e-05,
    "quartz": 1.25e-05
   },
   "where": "paper \u00a73.2",
   "whose": "theirs"
  },
  {
   "changes_geometry": false,
   "how": "the brine's self-diffusion, stated",
   "name": "D0",
   "unit": "m^2/s",
   "value": 2.3e-09,
   "where": "paper \u00a72.3",
   "whose": "theirs"
  },
  {
   "changes_geometry": false,
   "how": "the paper states no bulk T2; 3.0 s is ours, applied at replay and not in the walk, and the reproduction reports the log-mean over 2.4-3.1 s as well",
   "name": "T2B",
   "unit": "s",
   "value": 3.0,
   "where": "not in the paper",
   "whose": "ours"
  },
  {
   "changes_geometry": false,
   "how": "non-negative least squares with a second-difference penalty on 60 points from 1 ms, applied to THEIR released train and to ours identically, so the two sides of the comparison share the estimator even though it is not theirs",
   "name": "T2 inversion",
   "unit": "-",
   "value": "non-negative least squares with a second-difference penalty, lam = 0.1 (t2_distribution)",
   "where": "the paper states its own only as a regularised inversion",
   "whose": "ours"
  },
  {
   "changes_geometry": false,
   "how": "the boundary local time is stored as a channel and weighted at replay; their walk kills a walker at an attempted move into a grain voxel. The two agree in the continuum limit",
   "name": "surface rule",
   "unit": "-",
   "value": "exp(-2 (rho/D) d_perp) per reflection",
   "where": "the walk",
   "whose": "ours"
  }
 ],
 "previous_sha256": "4ad52625c812a8f904e346b41e1f6793b8418f430fddc402abe67c5111813023",
 "published_kind": "data",
 "quantities": [
  {
   "direct": {
    "grid": {
     "from_s": 0.001,
     "kind": "log",
     "n": 60,
     "sample_ms": 1.0,
     "solver": "non-negative least squares with a second-difference penalty, lam = 0.1 (t2_distribution)",
     "to_s": 10.0
    },
    "n_walkers": 200000,
    "se": 0.001101402177425109,
    "se_derivation": "the delta method over walkers on the log-mean (talabi_micro_ct_rocks.log_mean_gradient), MEASURED at record time on this family's own 6_q100.rpk -- 0.001366 over 130,000 walkers at the same rho, channel and grid -- and scaled to the direct walk's 200,000 by 1/sqrt(N) (x 0.806226). The direct walk's own per-walker decays were not retained; the relative per-echo spread is a property of the substrate and the estimator, not of the pack",
    "se_kind": "delta_method",
    "solver": "non-negative least squares with a second-difference penalty, lam = 0.1 (t2_distribution)",
    "source": "examples/validation/ling_sand_packs.py, recorded in this family's direct.json by the DIRECT fused-engine walk at the walker count and step stated with it; that walk is read, never repeated",
    "unit": "ms",
    "value": 856.54
   },
   "documents": {
    "10.1007/s11242-022-01764-w": {
     "agency": "crossref",
     "container": "Transport in Porous Media",
     "doi": "10.1007/s11242-022-01764-w",
     "resolved": "2026-09-27T01:17:40Z",
     "title": "Model Synthetic Samples for Validation of NMR Signal Simulations",
     "type": "journal-article"
    }
   },
   "name": "T2_log_mean",
   "published": {
    "data_sha256": "a9e09a21776d4c3f2c24f017547e75da1322ae19251569017f8b0c480d716eae",
    "data_url": "https://doi.org/10.6084/m9.figshare.17161730",
    "document": "10.1007/s11242-022-01764-w",
    "locator": "the log-mean of the released te = 100 us CPMG train of sample 6_Q100, inverted on the 1 ms grid with the same estimator as ours",
    "printed_in": "Model Synthetic Samples for Validation of NMR Signal Simulations (Ling et al. 2022), whose released te = 100 us echo train the value is read from",
    "uncertainty": 0.0,
    "uncertainty_is": "none stated: the paper prints no T2 value anywhere -- its comparison is Fig. 5, two distributions overlaid with no agreement metric -- and the released echo train carries no repeat, so the gate's budget rests on our own standard errors alone and the disagreement with them is recorded rather than failed on",
    "unit": "ms",
    "value": 727.084,
    "verbatim": ""
   },
   "substrate": "6_Q100"
  },
  {
   "direct": {
    "grid": {
     "from_s": 0.001,
     "kind": "log",
     "n": 60,
     "sample_ms": 1.0,
     "solver": "non-negative least squares with a second-difference penalty, lam = 0.1 (t2_distribution)",
     "to_s": 10.0
    },
    "n_walkers": 200000,
    "se": 0.002699867506755278,
    "se_derivation": "the delta method over walkers on the log-mean (talabi_micro_ct_rocks.log_mean_gradient), MEASURED at record time on this family's own 1_g100.rpk -- 0.003349 over 130,000 walkers at the same rho, channel and grid -- and scaled to the direct walk's 200,000 by 1/sqrt(N) (x 0.806226). The direct walk's own per-walker decays were not retained; the relative per-echo spread is a property of the substrate and the estimator, not of the pack",
    "se_kind": "delta_method",
    "solver": "non-negative least squares with a second-difference penalty, lam = 0.1 (t2_distribution)",
    "source": "examples/validation/ling_sand_packs.py, recorded in this family's direct.json by the DIRECT fused-engine walk at the walker count and step stated with it; that walk is read, never repeated",
    "unit": "ms",
    "value": 223.26
   },
   "documents": {
    "10.1007/s11242-022-01764-w": {
     "agency": "crossref",
     "container": "Transport in Porous Media",
     "doi": "10.1007/s11242-022-01764-w",
     "resolved": "2026-09-27T01:17:40Z",
     "title": "Model Synthetic Samples for Validation of NMR Signal Simulations",
     "type": "journal-article"
    }
   },
   "name": "T2_log_mean",
   "published": {
    "data_sha256": "0eb1de561db7930e31726105bd8f171e68a53db0997f8521f911c804c3093ebe",
    "data_url": "https://doi.org/10.6084/m9.figshare.17161730",
    "document": "10.1007/s11242-022-01764-w",
    "locator": "the log-mean of the released te = 100 us CPMG train of sample 1_G100, inverted on the 1 ms grid with the same estimator as ours",
    "printed_in": "Model Synthetic Samples for Validation of NMR Signal Simulations (Ling et al. 2022), whose released te = 100 us echo train the value is read from",
    "uncertainty": 0.0,
    "uncertainty_is": "none stated: the paper prints no T2 value anywhere -- its comparison is Fig. 5, two distributions overlaid with no agreement metric -- and the released echo train carries no repeat, so the gate's budget rests on our own standard errors alone and the disagreement with them is recorded rather than failed on",
    "unit": "ms",
    "value": 178.449,
    "verbatim": ""
   },
   "substrate": "1_G100"
  }
 ],
 "same_released_geometry": true,
 "sample": "the same physical object: the CPMG was measured on each pack, which was then resin-set and micro-CT imaged, and both halves are in the same deposit",
 "sample_relation": "the same object",
 "source_note": "Ling et al. 2022 (Transport in Porous Media 142:623-639) for the packs, the measured CPMG and the fitted relaxivities; the micro-CT lattices and the echo trains are both in the figshare deposit 10.6084/m9.figshare.17161730 (CC BY 4.0).",
 "stage": "reference",
 "title": "Model Synthetic Samples for Validation of NMR Signal Simulations",
 "title_matches": true
}