The degenerome-a novel streamline-wise approach for white matter integrity in neurodegeneration.

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Paper

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The authors' code

C++ · 115 lines · 3.6 KB · no license

/***************************************************************************************************************
Copyright (c) 2011, Marco Reisert, Valerij G. Kiselev, Medical Physics, University Medical Center Freiburg
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* Neither the name of the <organization> nor the
names of its contributors may be used to endorse or promote products
derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
****************************************************************************************************************/
#include <math.h>
#include "mex.h"
#include "matrix.h"
#define REAL float
void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[] )
{
if(nrhs!=2) {
mexPrintf("wrong usage!!\n",nrhs);
return;
} else if(nlhs>4) {
printf("Too many output arguments\n");
return;
}
int pcnt = 0;
const mxArray *Dim;
Dim = prhs[pcnt++];
REAL *dim = (REAL*) mxGetData(Dim);
int w = (int) dim[0];
int h = (int) dim[1];
int d = (int) dim[2];
const mxArray *Pts;
Pts = prhs[pcnt++];
const int numdim = mxGetNumberOfDimensions(Pts);
const unsigned long *pdims = mxGetDimensions(Pts);
int numPts = pdims[1];
REAL *pts = (REAL*) mxGetData(Pts);
unsigned long dims[3];
dims[0] = w;
dims[1] = h;
dims[2] = d;
plhs[0] = mxCreateNumericArray(3,dims,mxGetClassID(Dim),mxREAL);
REAL *accu = (REAL*) mxGetData(plhs[0]);
for (int i = 0; i < numPts; i++)
{
int idx = 3*i;
int px = (int) (pts[idx]);
if (px < 0 || px >= w-1)
continue;
int py = (int) (pts[idx+1]);
if (py < 0 || py >= h-1)
continue;
int pz = (int) (pts[idx+2]);
if (pz < 0 || pz >= d-1)
continue;
float frac_x = pts[idx ] - px;
float frac_y = pts[idx+1] - py;
float frac_z = pts[idx+2] - pz;
accu[px + w*(py+h*pz)] += (1-frac_x)*(1-frac_y)*(1-frac_z);
accu[px+1 + w*(py+h*pz)] += (frac_x)*(1-frac_y)*(1-frac_z);
accu[px + w*(py+1+h*pz)] += (1-frac_x)*(frac_y)*(1-frac_z);
accu[px + w*(py+h*pz+h)] += (1-frac_x)*(1-frac_y)*(frac_z);
accu[px + w*(py+1+h*pz+h)] += (1-frac_x)*(frac_y)*(frac_z);
accu[px+1 + w*(py+h*pz+h)] += (frac_x)*(1-frac_y)*(frac_z);
accu[px+1 + w*(py+1+h*pz)] += (frac_x)*(frac_y)*(1-frac_z);
accu[px+1 + w*(py+1+h*pz+h)] += (frac_x)*(frac_y)*(frac_z);
}
}

AccumulateBilin.cpp at commit 6b25763, no license · at the source

Overview

Authors: Jonas A Hosp¹, Marco Reisert^2,3, Nils Schröter¹, Elias Kellner², Hansjörg Mast⁴, Michel Rijntjes¹, Sabine Hellwig⁵, Lars Frings⁶, Heinz Wiendl¹, Horst Urbach⁴, Alexander Rau⁴

ORCID iDs: Nils Schröter, Lars Frings

Institutions: University of Freiburg (Germany); University Medical Center Freiburg (Germany)

Journal: NPJ Parkinson's disease, volume 12, issue 1, article 139

Dates: received 22 February 2026; accepted 1 June 2026; published online 10 June 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.1038/s41531-026-01428-2 · PMID 42271162 · PMCID PMC13254335 · OpenAlex W7164185736

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: structural MRI / diffusion (modality), human (organism), Parkinson's (population), clinical / translational (subfield)

Methods: Connectivity, Statistics, fMRI & imaging, Physiology & signal measures, Preprocessing

Keywords: Biomarkers, Neurology, Neuroscience

Topic: Advanced Neuroimaging Techniques and Applications (Radiology, Nuclear Medicine and Imaging, Medicine), according to OpenAlex

Funding: Deutsche Forschungsgemeinschaft (Priority Programme SPP2177, grant RA 3495)

Citations: not cited yet (Europe PMC); 66 references in the paper

Abstract

Neurodegenerative diseases impair both gray matter and long-range white-matter pathways. Existing diffusion MRI approaches are either local or depend on predefined parcellations, limiting their ability to capture distributed network disruption. We introduce a streamline-wise framework to map axonal degeneration and derive disease-specific fiber “degeneromes” across Alzheimer’s disease (AD), Parkinson’s disease (PD), multiple system atrophy (MSA), and progressive supranuclear palsy (PSP). We analyzed diffusion microstructure imaging and T1-weighted MRI (3 T Siemens Prisma, 2018–2024) in AD (n = 81), PD (n = 177), MSA (n = 50), PSP (n = 35), and healthy controls (n = 26). The intraaxonal volume fraction, estimated via a Bayesian three-compartment model, was mapped along ~20,000 normative streamlines in MNI space using age- and sex-adjusted regression with FDR correction. Streamline-wise mapping revealed disease-specific degeneromes consistent with established pathoanatomical models: AD involved limbic and temporo-occipital pathways, PD showed commissural and posterior association involvement, MSA affected pontocerebellar and corticospinal tracts, and PSP involved the dentato-rubro-thalamic tract and superior cerebellar peduncle. These signatures supported group-level differentiation, and streamline-wise z-scores enabled intuitive single-patient visualization. Fiber degeneromes offer a connectome-informed biomarker with strong biological plausibility, discriminatory potential across neurodegenerative entities, and a clear route toward clinical single-patient reporting.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above.

reisert/globaltracking

License: none: the authors keep all their rights

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: 6b257634cfd289d30e98481838e1c3bb2b65f056, 7 June 2023

Languages: MATLAB (84), C++ (15), C/C++ (1)

Size: 135 files, 100 scripts

Software Heritage: not archived

Found in: “Code availability”

Holds: README

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

Tools: Tools for NIfTI and ANALYZE image (MATLAB) (16 files), Image Processing Toolbox (3 files)

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

27 September 2026: the link answers

101 files

AccumulateBilin.cpp, C++, 115 lines
AccumulateBilinWeighted.cpp, C++, 122 lines
BuildFibres.cpp, C++, 370 lines
CreateConnectivityMatrixROI.cpp, C++, 239 lines
DPS_nifti_to_hardi.m, MATLAB, 115 lines
DPS_nifti_to_mrs.m, MATLAB, 55 lines
DPX_mrs_to_nifti.m, MATLAB, 324 lines
DPX_reslice_volume.m, MATLAB, 98 lines
EnergyComputerBase.cpp, C++, 405 lines
EnergyComputer_connec.cpp, C++, 348 lines
FunkRadonTrans.m, MATLAB, 54 lines
MersenneTwister.h, C/C++, 594 lines
ParticleGrid.cpp, C++, 639 lines
RJMCMCBase.cpp, C++, 291 lines
RJMCMC_randshift.cpp, C++, 706 lines
SphereInterpolator.cpp, C++, 148 lines
anisoDiffusion.cpp, C++, 160 lines
anisoDiffusionHomogenous.cpp, C++, 160 lines
auxilary_classes.cpp, C++, 661 lines
chooseThreshold_stackview.m, MATLAB, 153 lines
computeFiberCorrelation.m, MATLAB, 30 lines
cpmSH.m, MATLAB, 27 lines
createCM.m, MATLAB, 74 lines
createCM_GT.m, MATLAB, 56 lines
createStopButton.m, MATLAB, 21 lines
estimateWMmask.m, MATLAB, 24 lines
fiberGT_tool.m, MATLAB, 1,988 lines
fileexists.m, MATLAB, 10 lines
ft_make.m, MATLAB, 6 lines
ftr2FDmaps.m, MATLAB, 92 lines
genFDfromFTR.m, MATLAB, 70 lines
imresize3D_diff.m, MATLAB, 25 lines
make.m, MATLAB, 5 lines
mn_isvector.m, MATLAB, 58 lines
mrstruct_alternatives.m, MATLAB, 509 lines
mrstruct_checkin.m, MATLAB, 160 lines
mrstruct_convert.m, MATLAB, 260 lines
mrstruct_downcast_dimension.m, MATLAB, 175 lines
mrstruct_downcast_dimension_def.m, MATLAB, 146 lines
mrstruct_init.m, MATLAB, 207 lines
mrstruct_iscast.m, MATLAB, 63 lines
mrstruct_istype.m, MATLAB, 256 lines
mrstruct_query.m, MATLAB, 305 lines
mrstruct_read.m, MATLAB, 118 lines
mrstruct_type_ndims.m, MATLAB, 77 lines
mrstruct_upcast_dimension_def.m, MATLAB, 116 lines
mrstruct_write.m, MATLAB, 94 lines
nifti/affine.m, MATLAB, 554 lines
nifti/bipolar.m, MATLAB, 94 lines
nifti/bresenham_line3d.m, MATLAB, 189 lines
nifti/clip_nii.m, MATLAB, 115 lines
nifti/collapse_nii_scan.m, MATLAB, 260 lines
nifti/expand_nii_scan.m, MATLAB, 48 lines
nifti/extra_nii_hdr.m, MATLAB, 255 lines
nifti/flip_lr.m, MATLAB, 84 lines
nifti/get_nii_frame.m, MATLAB, 164 lines
nifti/load_nii.m, MATLAB, 198 lines
nifti/load_nii_ext.m, MATLAB, 216 lines
nifti/load_nii_hdr.m, MATLAB, 289 lines
nifti/load_nii_img.m, MATLAB, 392 lines
nifti/load_nii_xmlhdr.m, MATLAB, 73 lines
nifti/load_untouch0_nii_hdr.m, MATLAB, 200 lines
nifti/load_untouch_header_only.m, MATLAB, 187 lines
nifti/load_untouch_nii.m, MATLAB, 269 lines
nifti/load_untouch_nii_hdr.m, MATLAB, 217 lines
nifti/load_untouch_nii_img.m, MATLAB, 476 lines
nifti/make_ana.m, MATLAB, 210 lines
nifti/make_nii.m, MATLAB, 256 lines
nifti/mat_into_hdr.m, MATLAB, 83 lines
nifti/pad_nii.m, MATLAB, 142 lines
nifti/reslice_nii.m, MATLAB, 321 lines
nifti/rri_file_menu.m, MATLAB, 179 lines
nifti/rri_orient.m, MATLAB, 106 lines
nifti/rri_orient_ui.m, MATLAB, 251 lines
nifti/rri_select_file.m, MATLAB, 636 lines
nifti/rri_xhair.m, MATLAB, 92 lines
nifti/rri_zoom_menu.m, MATLAB, 33 lines
nifti/save_nii.m, MATLAB, 286 lines
nifti/save_nii_ext.m, MATLAB, 38 lines
nifti/save_nii_hdr.m, MATLAB, 227 lines
nifti/save_untouch0_nii_hdr.m, MATLAB, 219 lines
nifti/save_untouch_header_only.m, MATLAB, 71 lines
nifti/save_untouch_nii.m, MATLAB, 260 lines
nifti/save_untouch_nii_hdr.m, MATLAB, 295 lines
nifti/save_untouch_slice.m, MATLAB, 580 lines
nifti/unxform_nii.m, MATLAB, 40 lines
nifti/verify_nii_ext.m, MATLAB, 45 lines
nifti/view_nii.m, MATLAB, 4,873 lines
nifti/view_nii_menu.m, MATLAB, 480 lines
nifti/xform_nii.m, MATLAB, 521 lines
pcRJMCMC.cpp, C++, 388 lines
rebuildFibers.m, MATLAB, 27 lines
reparametrize_arclen.cpp, C++, 149 lines
saveFTR.m, MATLAB, 82 lines
smoothHardi.m, MATLAB, 9 lines
smoothODF.m, MATLAB, 10 lines
stackview.m, MATLAB, 110 lines
stopButtonOnTop.m, MATLAB, 3 lines
stopButtonPressed.m, MATLAB, 2 lines
write_mrtrix_tracks.m, MATLAB, 65 lines
README.md, Text, 16 lines

At the source: bitbucket.org/reisert/globaltracking

reisert/degenerome

License: none: the authors keep all their rights

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: cfe0c6de6d0cdb0afab6ee71f2642b436cd371bf, 23 January 2026

Size: 4 files, 0 scripts

Software Heritage: not archived

Found in: “Code availability”

Holds: README

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

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

27 September 2026: the link answers

1 file

README.md, Text, 44 lines

At the source: bitbucket.org/reisert/degenerome

Code availability

DMI parameter calculation was performed using the platform NORA (http://www.nora-imaging.org), with additional analyses based on CAT12/SPM-VBM and the publicly available global tracking toolbox (https://bitbucket.org/reisert/globaltracking). The normative tractogram used in this study, including sparse and dense reconstructions, is available at (https://bitbucket.org/reisert/degenerome).

Reproduced under the paper's license (CC BY), from the paper cited above.

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:

2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
100 scripts, each with its path and the digest of its content;
no match between paragraphs and code yet;
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.

Data availability

Data is available from the authors upon reasonable request and approval of the ethics committee.

Reproduced under the paper's license (CC BY), from the paper cited above.

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 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 3 keywords, 1 funder, 66 references.

Cite

This paper

Hosp, J. A., Reisert, M., Schröter, N., Kellner, E., Mast, H., Rijntjes, M., Hellwig, S., Frings, L., Wiendl, H., Urbach, H., & Rau, A. (2026). The degenerome-a novel streamline-wise approach for white matter integrity in neurodegeneration. NPJ Parkinson's disease, 12(1), 139. https://doi.org/10.1038/s41531-026-01428-2

BibTeX

@article{hosp2026degenerome, author = {Hosp, Jonas A and Reisert, Marco and Schröter, Nils and Kellner, Elias and Mast, Hansjörg and Rijntjes, Michel and Hellwig, Sabine and Frings, Lars and Wiendl, Heinz and Urbach, Horst and Rau, Alexander}, title = {{The degenerome-a novel streamline-wise approach for white matter integrity in neurodegeneration}}, journal = {NPJ Parkinson's disease}, year = {2026}, month = jun, volume = {12}, number = {1}, pages = {139}, publisher = {Nature Publishing Group}, issn = {2373-8057}, doi = {10.1038/s41531-026-01428-2}, url = {https://doi.org/10.1038/s41531-026-01428-2}, pmid = {42271162}, pmcid = {PMC13254335} }

RIS

TY - JOUR AU - Hosp, Jonas A AU - Reisert, Marco AU - Schröter, Nils AU - Kellner, Elias AU - Mast, Hansjörg AU - Rijntjes, Michel AU - Hellwig, Sabine AU - Frings, Lars AU - Wiendl, Heinz AU - Urbach, Horst AU - Rau, Alexander TI - The degenerome-a novel streamline-wise approach for white matter integrity in neurodegeneration T2 - NPJ Parkinson's disease J2 - NPJ Parkinsons Dis PY - 2026 DA - 2026/06/10 VL - 12 IS - 1 SP - 139 SN - 2373-8057 PB - Nature Publishing Group DO - 10.1038/s41531-026-01428-2 UR - https://doi.org/10.1038/s41531-026-01428-2 LA - en ER -

CSL-JSON

{ "id": "10.1038/s41531-026-01428-2", "type": "article-journal", "title": "The degenerome-a novel streamline-wise approach for white matter integrity in neurodegeneration", "container-title": "NPJ Parkinson's disease", "author": [ { "family": "Hosp", "given": "Jonas A" }, { "family": "Reisert", "given": "Marco" }, { "family": "Schröter", "given": "Nils" }, { "family": "Kellner", "given": "Elias" }, { "family": "Mast", "given": "Hansjörg" }, { "family": "Rijntjes", "given": "Michel" }, { "family": "Hellwig", "given": "Sabine" }, { "family": "Frings", "given": "Lars" }, { "family": "Wiendl", "given": "Heinz" }, { "family": "Urbach", "given": "Horst" }, { "family": "Rau", "given": "Alexander" } ], "container-title-short": "NPJ Parkinsons Dis", "volume": "12", "issue": "1", "page": "139", "DOI": "10.1038/s41531-026-01428-2", "PMID": "42271162", "PMCID": "PMC13254335", "ISSN": "2373-8057", "publisher": "Nature Publishing Group", "URL": "https://doi.org/10.1038/s41531-026-01428-2", "language": "en", "issued": { "date-parts": [ [ 2026, 6, 10 ] ] } }

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The degenerome-a novel streamline-wise approach for white matter integrity in neurodegeneration.

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reisert/globaltracking

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