Framework for Statistical Parametric Mapping of the Interactions between Glioblastoma Location, Treatment, Prognostic Variables, and Survival Using a Phase III Trial.

Code ↔ Paper

3 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 3 matches · all tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted

[1] § Materials and Methods › Non–voxel-wise models ↔ load_clinical_data.m, the whole file · a weak match · score 0.61 · methylation status, Baseline tumor volume, Age, MGMT, Tx, Treatment
[2] § Materials and Methods › Statistical models ↔ main_cox_atlas.m, the whole file · a weak match · score 0.59 · Cox proportional hazards, tumor presence, MATLAB, variables, covariates, mapping
[3] § Materials and Methods › Non–voxel-wise models ↔ load_clinical_data.m, the whole file · a weak match · score 0.58 · methylation status, baseline tumor volume, age, MGMT, treatment

Paper

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The authors' code

MATLAB · 59 lines · 2.1 KB · Apache-2.0 · 2 matches

function [patient_data, num_pat] = load_clinical_data(csvfile_name)
% LOAD_CLINICAL_DATA - Load patient demographics and clinical variables
%
% INPUTS:
% csvfile_name - (str) Path to csv file with the data or empty string to selectect it ''.
%
%
% OUTPUTS:
% patient_data - (matrix) Patient-level data from CSV file:
% Columns: [PatientID, SiteID, Age, Status, OS, Volume, Tx, MGMT]
% PatientID = Unique patient identifier
% SiteID = Trial site ID
% Age = Patient age (years)
% Status = 1 if alive (censored), 0 if death observed
% OS = Overall survival time (days)
% Volume = Baseline tumor volume (ml)
% Tx = Treatment arm (0/1)
% MGMT = MGMT methylation status
%
% num_pat - (integer) Number of patients included after filtering
%
% NOTES:
% Excludes patients with missing OS (overall survival)
% Open file dialog
if isempty(csvfile_name)
[file, path] = uigetfile('*.csv', 'Select the clinical CSV file',csvfile_name);
if isequal(file,0)
error('No file selected. Function aborted.');
end
filename = fullfile(path, file);
else
filename = csvfile_name;
end
% Load data
% orig_data = csvread(filename);
opts = detectImportOptions(filename, 'NumHeaderLines', 0);
T = readtable(filename, opts);
% Extract variables (assuming column names are standard)
PatientID = T.PatientID;
SiteID = T.SiteID;
Age = T.Age;
Status = T.Status;
OS = T.OS;
Volume = T.Volume;
Tx = T.Tx;
MGMT = T.MGMT;
% Combine into matrix
patient_data = [PatientID, SiteID, Age, Status, OS, Volume, Tx, MGMT];
% Remove rows with missing OS
valid_idx = ~isnan(OS);
patient_data = patient_data(valid_idx,:);
num_pat = size(patient_data,1);
fprintf('Loaded %d patients.\n', num_pat);
end

load_clinical_data.m at commit 4b81944, under Apache-2.0 · at the source

Overview

Authors: Francesco Sanvito^1,2, Catalina Raymond^1,2, Donatello Telesca³, Jingwen Yao^1,2, Lauren E Abrey⁴, Josep Garcia⁵, Brian Simmons⁵, Olivier Chinot⁶, Frank Saran⁷, Ryo Nishikawa⁸, Roger Henriksson⁹, Warren P Mason¹⁰, Wolfgang Wick¹¹, Timothy F Cloughesy¹², Benjamin M Ellingson^1,2

ORCID iDs: Francesco Sanvito, Catalina Raymond, Donatello Telesca, Jingwen Yao, Lauren E Abrey, Josep Garcia, Brian Simmons, Olivier Chinot, Frank Saran, Ryo Nishikawa, Roger Henriksson, Warren P Mason, Wolfgang Wick, Timothy F Cloughesy, Benjamin M Ellingson

Institutions: University of California, Los Angeles (United States); Roche (Switzerland) (Switzerland); Genentech; Aix-Marseille Université (France); Assistance Publique Hôpitaux de Marseille (France); Hôpital de la Timone (France); Royal Marsden NHS Foundation Trust (United Kingdom); Saitama Medical University (Japan); Umeå University (Sweden); Princess Margaret Cancer Centre (Canada); German Cancer Research Center (Germany); Heidelberg University (Germany); Deutsches Konsortium für Translationale Krebsforschung (Germany)

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research, volume 32, issue 11, pages 2230-2242

Dates: received 18 November 2025; accepted 11 March 2026; published online 16 March 2026; in print 1 June 2026

Type: Research article · Language: English

License: CC BY-NC-ND

Identifiers: DOI 10.1158/1078-0432.ccr-25-4419 · PMID 41837753 · PMCID PMC13223549 · OpenAlex W7137351942

Open access: hybrid, a free copy (OpenAlex)

Status: code verified

Categories: structural MRI / diffusion (modality), human (organism), other condition (population), clinical / translational (subfield)

Methods: Connectivity, Statistics

MeSH: Brain Neoplasms*, Glioblastoma*, Adult, Aged, Bevacizumab, Chemoradiotherapy, Female, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Prognosis, Proportional Hazards Models, Treatment Outcome (* major topic)

Topic: Glioma Diagnosis and Treatment (Genetics, Medicine), according to OpenAlex

Funding: U.S. Department of Defense (DOD) (CA220732); Foundation for the National Institutes of Health (R01CA279984, P50CA211015, R01CA270027)

Citations: not cited yet (Europe PMC); 68 references in the paper

Research resources: using the FMRIB Software Library RRID:SCR_002823, RRID:SCR_008624

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 3 matches between paragraphs and lines of code.

BTIL-UCLA/COX_open

License: Apache-2.0

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: 4b819443b75adbeaf5d358210654523ad07d7ebe, 20 January 2026

Languages: MATLAB (47), Python (1)

Size: 57 files, 48 scripts

Software Heritage: not checked

Found in: “Data Availability”

Holds: README, license file

Not found: CITATION.cff, environment file, tests, continuous integration, documentation

Tools: Tools for NIfTI and ANALYZE image (MATLAB) (14 files), Image Processing Toolbox (1 file), Parallel Computing Toolbox (1 file), NiBabel (1 file), NumPy (1 file), SciPy (1 file)

Availability: 1 check, the latest on 27 September 2026: the link answers

27 September 2026: the link answers

50 files

NIfTI_20140122/affine.m, MATLAB, 554 lines
NIfTI_20140122/bipolar.m, MATLAB, 94 lines
NIfTI_20140122/bresenham_line3d.m, MATLAB, 189 lines
NIfTI_20140122/clip_nii.m, MATLAB, 115 lines
NIfTI_20140122/collapse_nii_scan.m, MATLAB, 260 lines
NIfTI_20140122/expand_nii_scan.m, MATLAB, 48 lines
NIfTI_20140122/extra_nii_hdr.m, MATLAB, 255 lines
NIfTI_20140122/flip_lr.m, MATLAB, 84 lines
NIfTI_20140122/get_nii_frame.m, MATLAB, 164 lines
NIfTI_20140122/load_nii.m, MATLAB, 198 lines
NIfTI_20140122/load_nii_ext.m, MATLAB, 207 lines
NIfTI_20140122/load_nii_hdr.m, MATLAB, 280 lines
NIfTI_20140122/load_nii_img.m, MATLAB, 392 lines
NIfTI_20140122/load_untouch0_nii_hdr.m, MATLAB, 200 lines
NIfTI_20140122/load_untouch_header_only.m, MATLAB, 187 lines
NIfTI_20140122/load_untouch_nii.m, MATLAB, 191 lines
NIfTI_20140122/load_untouch_nii_hdr.m, MATLAB, 217 lines
NIfTI_20140122/load_untouch_nii_img.m, MATLAB, 468 lines
NIfTI_20140122/make_ana.m, MATLAB, 210 lines
NIfTI_20140122/make_nii.m, MATLAB, 256 lines
NIfTI_20140122/mat_into_hdr.m, MATLAB, 83 lines
NIfTI_20140122/pad_nii.m, MATLAB, 142 lines
NIfTI_20140122/reslice_nii.m, MATLAB, 321 lines
NIfTI_20140122/rri_file_menu.m, MATLAB, 179 lines
NIfTI_20140122/rri_orient.m, MATLAB, 106 lines
NIfTI_20140122/rri_orient_ui.m, MATLAB, 251 lines
NIfTI_20140122/rri_select_file.m, MATLAB, 636 lines
NIfTI_20140122/rri_xhair.m, MATLAB, 92 lines
NIfTI_20140122/rri_zoom_menu.m, MATLAB, 33 lines
NIfTI_20140122/save_nii.m, MATLAB, 286 lines
NIfTI_20140122/save_nii_ext.m, MATLAB, 38 lines
NIfTI_20140122/save_nii_hdr.m, MATLAB, 227 lines
NIfTI_20140122/save_untouch0_nii_hdr.m, MATLAB, 219 lines
NIfTI_20140122/save_untouch_header_only.m, MATLAB, 71 lines
NIfTI_20140122/save_untouch_nii.m, MATLAB, 232 lines
NIfTI_20140122/save_untouch_nii_hdr.m, MATLAB, 207 lines
NIfTI_20140122/save_untouch_slice.m, MATLAB, 580 lines
NIfTI_20140122/unxform_nii.m, MATLAB, 40 lines
NIfTI_20140122/verify_nii_ext.m, MATLAB, 45 lines
NIfTI_20140122/view_nii.m, MATLAB, 4,873 lines
NIfTI_20140122/view_nii_menu.m, MATLAB, 480 lines
NIfTI_20140122/xform_nii.m, MATLAB, 521 lines
calculate_p_for_combined_coefficient.py, Python, 132 lines
load_clinical_data.m, MATLAB, 59 lines, 2 matches
main_cox_atlas.m, MATLAB, 83 lines, 1 match
prepare_slice_files.m, MATLAB, 67 lines
run_voxelwise_cox.m, MATLAB, 281 lines
save_nifti_maps.m, MATLAB, 97 lines
LICENSE, License, 201 lines
README.md, Text, 209 lines

At the source: github.com/BTIL-UCLA/COX_open

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
48 scripts, each with its path and the digest of its content;
3 matches between paragraphs of the paper and lines of the code (method lexical-v1);
neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

it points to the authors' code: BTIL-UCLA/COX_open
it says that the data are available on request

Read it in the paper: doi.org/10.1158/1078-0432.ccr-25-4419.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 2, 28 September 2026

Publisher: n/a → American Association for Cancer Research

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 15 authors, 14 MeSH terms, 2 funders, 65 references, 2 RRIDs.

Cite

This paper

Sanvito, F., Raymond, C., Telesca, D., Yao, J., Abrey, L. E., Garcia, J., Simmons, B., Chinot, O., Saran, F., Nishikawa, R., Henriksson, R., Mason, W. P., Wick, W., Cloughesy, T. F., & Ellingson, B. M. (2026). Framework for Statistical Parametric Mapping of the Interactions between Glioblastoma Location, Treatment, Prognostic Variables, and Survival Using a Phase III Trial. Clinical cancer research : an official journal of the American Association for Cancer Research, 32(11), 2230-2242. https://doi.org/10.1158/1078-0432.ccr-25-4419

BibTeX

@article{sanvito2026framework, author = {Sanvito, Francesco and Raymond, Catalina and Telesca, Donatello and Yao, Jingwen and Abrey, Lauren E and Garcia, Josep and Simmons, Brian and Chinot, Olivier and Saran, Frank and Nishikawa, Ryo and Henriksson, Roger and Mason, Warren P and Wick, Wolfgang and Cloughesy, Timothy F and Ellingson, Benjamin M}, title = {{Framework for Statistical Parametric Mapping of the Interactions between Glioblastoma Location, Treatment, Prognostic Variables, and Survival Using a Phase III Trial}}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, year = {2026}, month = jun, volume = {32}, number = {11}, pages = {2230--2242}, publisher = {American Association for Cancer Research}, issn = {1078-0432}, doi = {10.1158/1078-0432.ccr-25-4419}, url = {https://doi.org/10.1158/1078-0432.ccr-25-4419}, pmid = {41837753}, pmcid = {PMC13223549} }

RIS

TY - JOUR AU - Sanvito, Francesco AU - Raymond, Catalina AU - Telesca, Donatello AU - Yao, Jingwen AU - Abrey, Lauren E AU - Garcia, Josep AU - Simmons, Brian AU - Chinot, Olivier AU - Saran, Frank AU - Nishikawa, Ryo AU - Henriksson, Roger AU - Mason, Warren P AU - Wick, Wolfgang AU - Cloughesy, Timothy F AU - Ellingson, Benjamin M TI - Framework for Statistical Parametric Mapping of the Interactions between Glioblastoma Location, Treatment, Prognostic Variables, and Survival Using a Phase III Trial T2 - Clinical cancer research : an official journal of the American Association for Cancer Research J2 - Clin Cancer Res PY - 2026 DA - 2026/06/01 VL - 32 IS - 11 SP - 2230 EP - 2242 SN - 1078-0432 PB - American Association for Cancer Research DO - 10.1158/1078-0432.ccr-25-4419 UR - https://doi.org/10.1158/1078-0432.ccr-25-4419 LA - en ER -

CSL-JSON

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