Multi-voxel MR-spectroscopy signatures and associations with EEG network hyperexcitability and clinical symptomatology in borderline personality disorder.
The 1 match
- [1] § Methods › Magnetic resonance spectroscopy analysis and quality checks ↔ python/avg_q/mne.py, lines 49–87 · score 0.55 · FreeSurfer, MRI, volume, command, voxel, fitting
Paper
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The authors' code
Python · 102 lines · 4 KB · GPL-3.0 · 1 match
- import numpy
- import mne
- def to_Evokeds(epochs, montage='standard_1020'):
- '''epochs is a list of epochs as avg_q.numpy_Script epochs
- '''
- evokeds=[]
- for epoch in epochs:
- info=mne.create_info(ch_names=epoch.channelnames,sfreq=epoch.sfreq,ch_types='eeg')
- # cf https://mne.tools/dev/generated/mne.EvokedArray.html#mne.EvokedArray
- ev=mne.EvokedArray(
- epoch.data.transpose(),
- info,
- tmin= -epoch.beforetrig/epoch.sfreq,
- comment=epoch.comment,
- nave=epoch.nrofaverages,
- kind='average')
- ev.set_montage(montage)
- evokeds.append(ev)
- return evokeds
- def mne_Epochsource(mne_epochs):
- import avg_q.numpy_Script
- epochs=[]
- for thisepoch in mne_epochs:
- epoch=avg_q.numpy_Script.numpy_epoch(thisepoch.data.transpose())
- epoch.sfreq=thisepoch.info['sfreq']
- epoch.beforetrig= -round(thisepoch.tmin*thisepoch.info['sfreq'])
- epoch.nrofaverages=thisepoch.nave
- epoch.comment=' '.join([thisepoch.comment,thisepoch.get_channel_types()[0]])
- epoch.channelnames=thisepoch.ch_names
- epoch.channelpos=[x[:3] for x in mne.channels.find_layout(thisepoch.info).pos]
- epochs.append(epoch)
- epochsource=avg_q.numpy_Script.numpy_Epochsource(epochs)
- return epochsource
- def SphereSourceSpace_coords(circle_divisions=25, percentage=85):
- # Iter to yield theta and phi coordinates regularly distributed on a sphere
- # (open at the bottom towards theta=90° by 100-percentage)
- # This is separated out to reconstruct those coordinates later if needed
- dphi=numpy.pi/circle_divisions
- for theta in numpy.arange(dphi,numpy.pi*percentage/100,dphi):
- rdphi=dphi/numpy.sin(theta)
- # Correct this angle to avoid irregular (too close) distances between first and last point
- rdphi=2*numpy.pi/numpy.round(2*numpy.pi/rdphi)
- for phi in numpy.arange(0,2*numpy.pi,rdphi):
- yield (theta,phi)
- def make_SphereSourceSpace(sphereHM, radius=80, circle_divisions=25, percentage=85):
- '''sphereHM is a fitted spherical head model (mne.make_sphere_model)
- circle_divisions defines the number of sources on a full circle
- percentage is the coverage of the full sphere, leaving out part of its bottom
- '''
- # Try to approximate sources on a sphere surface by using "exclude"
- # Actually mne.setup_source_space() is for distributing sources on a surface
- # but requires FreeSurfer files
- # Source in /usr/lib/python3.11/site-packages/mne/source_space/_source_space.py
- #src1 = mne.setup_volume_source_space(sphere=sphere, pos=10.0, exclude=76) # 10mm grid
- # src is a 1-element list of dict, 'rr' contains the coordinates of *all* originally created sources
- # 'inuse' defines which are actually used
- r=radius/1000
- rr=numpy.array([
- (r*numpy.sin(theta)*numpy.sin(phi),r*numpy.sin(theta)*numpy.cos(phi),r*numpy.cos(theta))
- for theta,phi in SphereSourceSpace_coords(circle_divisions, percentage)
- ])
- np=rr.shape[0]
- ssdict={
- 'type': 'discrete',
- 'coord_frame': mne._fiff.constants.FIFF.FIFFV_COORD_MRI,
- 'id': mne._fiff.constants.FIFF.FIFFV_MNE_SURF_UNKNOWN,
- 'np': np,
- 'nuse': np,
- 'rr': rr+sphereHM['r0'],
- 'inuse': numpy.full((np,),True),
- 'nn': numpy.array([[0,0,1]]).repeat(np,axis=0),
- 'vertno': numpy.arange(np),
- 'neighbor_vert': numpy.array([[-1]*26]).repeat(np,axis=0),
- 'ntri': 0,
- 'use_tris': None,
- 'nearest': None,
- 'dist': None,
- #'src_mri_t': mne.source_space._source_space._make_voxel_ras_trans(move=numpy.array([0,0,0]),voxel_size=numpy.ones(3),ras=numpy.eye(3)),
- }
- import os
- return mne.SourceSpaces([ssdict], dict(working_dir=os.getcwd(), command_line="None"))
- def VolSourceToEvoked(stc, src, r0, ev):
- info=mne.create_info(stc.shape[0], stc.sfreq, ch_types='eeg')
- source_ev=mne.EvokedArray(
- stc.data,
- info,
- tmin=stc.tmin,
- comment=ev.comment,
- nave=ev.nave,
- kind='average')
- montage=ev.get_montage()
- ch_pos={ch_name: src[0]['rr'][int(ch_name)]-r0 for ch_name in source_ev.ch_names}
- dig=mne.channels.make_dig_montage(ch_pos=ch_pos, nasion=montage.dig[1]['r'], lpa=montage.dig[0]['r'], rpa=montage.dig[2]['r'], hsp=None, hpi=None, coord_frame='head')
- source_ev.set_montage(dig)
- return source_ev
mne.py at commit c90c29c, under GPL-3.0 · at the source
Overview
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Psychology, Laboratory for Biological Psychology, Clinical Psychology and Psychotherapy - University of Freiburg, Freiburg, Germany
- German Center for Mental Health (DZPG), Partner Site Berlin/Potsdam, Berlin, Germany
- Division of Medical Physics, Department of Diagnostic and Interventional Radiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Berlin, Germany
- Department of Stereotactic and Functional Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
Abstract
Introduction: Previous studies have reported altered gamma-aminobutyric acid (GABA) and glutamate levels in borderline personality disorder (BPD), suggesting disruptions in excitatory-inhibitory neurotransmission. Electroencephalographic (EEG) research has indicated potential network hyperexcitability in BPD, evidenced by increased intermittent rhythmic delta and theta activity (IRDA/
Methods: Sixty-six female patients diagnosed with BPD (mean age: 30.2 ± 9.7 years) and 29 age-matched female healthy controls (mean age: 27.8 ± 8.0 years) received spirally encoded 3D MRSI scans. GABA, glutamate plus glutamine (Glx), total creatine (tCr) and total N-acetylaspartate (tNAA) were quantified and reported as ratios relative to tNAA and/
Results: No metabolite ratio showed a significant BPD vs. control difference. In BPD, IRDA/
Discussion: While no robust group differences emerged, mixed-models using continuous predictors linked higher Glx ratios in nucleus accumbens/
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.
berndf/avg_q
c90c29cd7061fc17ca95f082d23bf5765a696b4d, 3 September 2026Availability: 1 check, the latest on 30 September 2026: the link answers
- 30 September 2026: the link answers
494 files
- Documentation/
Create_Graphs.R , R, 36 lines - Documentation/
plot_fftfilter.R , R, 38 lines - TestSuite/
t_test_check.R , R, 36 lines - avg_q.c, C, 327 lines
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avg_q/ , Python, 99 linesSleep/ freiburg_setup.py - python/
avg_q/ , Python, 332 linesSleep/ sleep_eeg.py - python/
avg_q/ , Python, 137 linesSleep/ sleep_file.py - python/
avg_q/ , Python, 425 linesSleep/ slfile.py - python/
avg_q/ , Python, 134 linesSleep/ slplot.py - python/
avg_q/ , Python, 123 linesUnisens.py - python/
avg_q/ , Python, 21 lines__init__.py - python/
avg_q/ , Python, 467 linesavg_q.py - python/
avg_q/ , Python, 233 linesavg_q_file.py - python/
avg_q/ , Python, 17 lineschannelnames2channelpos. py - python/
avg_q/ , Python, 53 lineseeglab.py - python/
avg_q/ , Python, 705 linesfMRI_Correct.py - python/
avg_q/ , Python, 57 linesidircache.py - python/
avg_q/ , Python, 102 lines, 1 matchmne.py - python/
avg_q/ , Python, 75 linesnirs.py - python/
avg_q/ , Python, 318 linesnumpy_Script.py - python/
avg_q/ , Python, 295 linesparadigm.py - python/
avg_q/ , Python, 145 linesregressors.py - python/
avg_q/ , Python, 142 linest_detector.py - python/
avg_q/ , Python, 193 linestrgfile.py - python/
avg_q/ , Python, 51 linesunittests.py - python/
avg_q_unittests.py , Python, 204 lines - python/
voglps.py , Python, 60 lines - python/
voglps2svg.py , Python, 48 lines - python/
voglps2svg_cairo.py , Python, 45 lines - readymade/
ascaverage.c , C, 372 lines - readymade/
asccalc.c , C, 179 lines - readymade/
distance_correct.c , C, 226 lines - readymade/
spline_gridder.c , C, 371 lines - readymade/
swap_xz.c , C, 125 lines - vogl/
drivers/ , C, 571 linesNeXT.c - vogl/
drivers/ , C, 1,277 linesX11.c - vogl/
drivers/ , C, 583 linesapollo.c - vogl/
drivers/ , C, 582 linesdecX11.c - vogl/
drivers/ , C, 655 linesgrx.c - vogl/
drivers/ , C, 442 lineshpdxy.c - vogl/
drivers/ , C, 176 linesibmpc/ cga.c - vogl/
drivers/ , C, 125 linesibmpc/ ega.c - vogl/
drivers/ , C, 159 linesibmpc/ hgc.c - vogl/
drivers/ , C, 1,062 linesibmpc/ mswin.c - vogl/
drivers/ , C/C++, 7 linesibmpc/ mswin.h - vogl/
drivers/ , C, 165 linesibmpc/ pc_fill.c - vogl/
drivers/ , C, 14 linesibmpc/ pc_getke.c - vogl/
drivers/ , C, 31 linesibmpc/ pc_locat.c - vogl/
drivers/ , C, 139 linesibmpc/ pc_text.c - vogl/
drivers/ , C, 33 linesibmpc/ setmode.c - vogl/
drivers/ , C, 151 linesibmpc/ sigma.c - vogl/
drivers/ , C, 31 linesibmpc/ vega_col.c - vogl/
drivers/ , C, 19 linesibmpc/ vega_dra.c - vogl/
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drivers/ , C, 127 linesibmpc/ vga.c - vogl/
drivers/ , C, 664 linesps.c - vogl/
drivers/ , C, 908 linessun.c - vogl/
drivers/ , C, 449 linestek.c - vogl/
drivers/ , C++, 370 lineswxwin.cpp - vogl/
examples/ , C, 169 linesballs.c - vogl/
examples/ , C, 164 linescirctxt.c - vogl/
examples/ , C, 165 linescube.c - vogl/
examples/ , C, 194 linescurves.c - vogl/
examples/ , C, 186 lineslcube.c - vogl/
examples/ , C, 85 linesloc.c - vogl/
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examples/ , C, 176 linesmoretxt2.c - vogl/
examples/ , C, 170 linesmswin/ balls.c - vogl/
examples/ , C, 165 linesmswin/ circtxt.c - vogl/
examples/ , C, 166 linesmswin/ cube.c - vogl/
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examples/ , C, 202 linesmswin/ lcube.c - vogl/
examples/ , C, 86 linesmswin/ loc.c - vogl/
examples/ , C, 218 linesmswin/ moretxt.c - vogl/
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examples/ , C, 197 linesmswin/ objvws.c - vogl/
examples/ , C, 285 linesmswin/ patches.c - vogl/
examples/ , C, 196 linesmswin/ poly.c - vogl/
examples/ , C, 159 linesmswin/ shapes.c - vogl/
examples/ , C, 93 linesmswin/ simple.c - vogl/
examples/ , C, 81 linesmswin/ sinewave.c - vogl/
examples/ , C, 499 linesmswin/ teapot.c - vogl/
examples/ , C, 181 linesmswin/ tetra.c - vogl/
examples/ , C, 165 linesmswin/ tmesh.c - vogl/
examples/ , C, 55 linesmswin/ trivial.c - vogl/
examples/ , C, 190 linesmswin/ views.c - vogl/
examples/ , C/C++, 7 linesmswin/ voglwin.h - vogl/
examples/ , C, 166 linesmswin/ world.c - vogl/
examples/ , C, 196 linesobjvws.c - vogl/
examples/ , C, 284 linespatches.c - vogl/
examples/ , C, 195 linespoly.c - vogl/
examples/ , C, 158 linesshapes.c - vogl/
examples/ , C, 92 linessimple.c - vogl/
examples/ , C, 80 linessinewave.c - vogl/
examples/ , C, 220 linesstetra.c - vogl/
examples/ , C, 141 linessunview/ balls.c - vogl/
examples/ , C, 91 linessunview/ lcube.c - vogl/
examples/ , C, 73 linessunview/ svballs.c - vogl/
examples/ , C, 255 linessunview/ svlcube.c - vogl/
examples/ , C, 498 linesteapot.c - vogl/
examples/ , C, 180 linestetra.c - vogl/
examples/ , C, 165 linestmesh.c - vogl/
examples/ , C, 54 linestrivial.c - vogl/
examples/ , C, 189 linesviews.c - vogl/
examples/ , C, 165 linesworld.c - vogl/
examples/ , C, 144 linesxt/ balls.c - vogl/
examples/ , C, 91 linesxt/ lcube.c - vogl/
examples/ , C, 110 linesxt/ xtballs.c - vogl/
examples/ , C, 271 linesxt/ xtlcube.c - vogl/
examples/ , C, 141 linesxview/ balls.c - vogl/
examples/ , C, 91 linesxview/ lcube.c - vogl/
examples/ , C, 120 linesxview/ xvballs.c - vogl/
examples/ , C, 397 linesxview/ xvlcube.c - vogl/
hershey/ , C, 18 linessrc/ check.c - vogl/
hershey/ , C, 66 linessrc/ fdisp.c - vogl/
hershey/ , C, 451 linessrc/ fhtext.c - vogl/
hershey/ , MATLAB, not shown heresrc/ futura.m - vogl/
hershey/ , C, 58 linessrc/ getchar.c - vogl/
hershey/ , C, 196 linessrc/ h2v.c - vogl/
hershey/ , C/C++, 243 linessrc/ h2v.h - vogl/
hershey/ , C, 23 linessrc/ halloc.c - vogl/
hershey/ , C, 133 linessrc/ hdisp.c - vogl/
hershey/ , C, 718 linessrc/ htext.c - vogl/
hershey/ , R, not shown heresrc/ times.r - vogl/
src/ , C, 379 linesarcs.c - vogl/
src/ , C, 95 linesattr.c - vogl/
src/ , C, 137 linesbuffer.c - vogl/
src/ , C, 143 linesclip.c - vogl/
src/ , C, 279 linescurves.c - vogl/
src/ , C, 296 linesdraw.c - vogl/
src/ , C, 703 linesdrivers.c - vogl/
src/ , C/C++, 57 linesfvodevic.h - vogl/
src/ , C/C++, 57 linesfvodevice.h - vogl/
src/ , C/C++, 20 linesfvogl.h - vogl/
src/ , C, 33 linesgetgp.c - vogl/
src/ , C, 122 lineslines.c - vogl/
src/ , C, 43 linesmapping.c - vogl/
src/ , C, 298 linesmatrix.c - vogl/
src/ , C, 60 linesminv4.c - vogl/
src/ , C, 195 linesmove.c - vogl/
src/ , C, 26 linesmsfort/ zap_c.c - vogl/
src/ , C, 43 linesnewtoken.c - vogl/
src/ , C, 44 linesnewtokens.c - vogl/
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src/ , C, 472 linespatches.c - vogl/
src/ , C, 109 linespoints.c - vogl/
src/ , C, 1,114 linespolygons.c - vogl/
src/ , C, 66 linespref.c - vogl/
src/ , C, 413 linesqueue.c - vogl/
src/ , C, 99 linesrect.c - vogl/
src/ , C, 48 linesscale.c - vogl/
src/ , C, 166 linessunfort/ farcs.c - vogl/
src/ , C, 37 linessunfort/ fattr.c - vogl/
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src/ , C, 96 linessunfort/ fbuffer.c - vogl/
src/ , C, 102 linessunfort/ fcurves.c - vogl/
src/ , C, 121 linessunfort/ fdraw.c - vogl/
src/ , C, 429 linessunfort/ fdrivers.c - vogl/
src/ , C, 31 linessunfort/ fgetgp.c - vogl/
src/ , C, 51 linessunfort/ flines.c - vogl/
src/ , C, 97 linessunfort/ fmatrix.c - vogl/
src/ , C, 120 linessunfort/ fmove.c - vogl/
src/ , C, 106 linessunfort/ fobjects.c - vogl/
src/ , C, 103 linessunfort/ fpatches.c - vogl/
src/ , C, 62 linessunfort/ fpoints.c - vogl/
src/ , C, 442 linessunfort/ fpoly.c - vogl/
src/ , C, 41 linessunfort/ fpref.c - vogl/
src/ , C, 103 linessunfort/ fqueue.c - vogl/
src/ , C, 55 linessunfort/ frect.c - vogl/
src/ , C, 205 linessunfort/ ftext.c - vogl/
src/ , C, 66 linessunfort/ ftrans.c - vogl/
src/ , C, 177 linessunfort/ fvcalls.c - vogl/
src/ , C, 78 linessunfort/ fviewing.c - vogl/
src/ , C, 70 linessunfort/ fviewp.c - vogl/
src/ , C, 11 linessunfort/ fyobbarays.c - vogl/
src/ , C, 85 linestensor.c - vogl/
src/ , C, 273 linestext.c - vogl/
src/ , C, 185 linestrans.c - vogl/
src/ , C, 21 linesvalloc.c - vogl/
src/ , C, 296 linesvcalls.c - vogl/
src/ , C, 31 linesvgui_hook.c - vogl/
src/ , C, 258 linesviewing.c - vogl/
src/ , C, 177 linesviewp.c - vogl/
src/ , C/C++, 104 linesvodevice.h - vogl/
src/ , C/C++, 694 linesvogl.h - vogl/
src/ , C, 29 linesyobbarays.c - COPYING, License, 674 lines
- README.md, Text, 48 lines
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;
- 492 scripts, each with its path and the digest of its content;
- 1 match 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.
Data availability statement
The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.
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, 30 September 2026: the first record
Recorded: type, language, journal, volume, pages, dates, 13 authors, 7 keywords, 64 references.
Cite
This paper
Schlump, A., Feige, B., Matthies, S., von Zedtwitz, K., Matteit, I., Nickel, K., Domschke, K., Reisert, M., Lange, T., Heinrichs, M., Endres, D., Tebartz van Elst, L., & Maier, S. (2026). Multi-voxel MR-spectroscopy signatures and associations with EEG network hyperexcitability and clinical symptomatology in borderline personality disorder. Frontiers in psychiatry, 17, 1708563. https://
BibTeX
@article{schlump2026mult
author = {Schlump, Andrea and Feige, Bernd and Matthies, Swantje and von Zedtwitz, Katharina and Matteit, Isabelle and Nickel, Kathrin and Domschke, Katharina and Reisert, Marco and Lange, Thomas and Heinrichs, Markus and Endres, Dominique and Tebartz van Elst, Ludger and Maier, Simon},
title = {{Multi-voxel MR-spectroscopy signatures and associations with EEG network hyperexcitability and clinical symptomatology in borderline personality disorder}},
journal = {Frontiers in psychiatry},
year = {2026},
month = mar,
volume = {17},
pages = {1708563},
publisher = {Frontiers Media SA},
issn = {1664-0640},
doi = {10.3389/
url = {https://
pmid = {41908118},
pmcid = {PMC13022906}
}
RIS
TY - JOUR
AU - Schlump, Andrea
AU - Feige, Bernd
AU - Matthies, Swantje
AU - von Zedtwitz, Katharina
AU - Matteit, Isabelle
AU - Nickel, Kathrin
AU - Domschke, Katharina
AU - Reisert, Marco
AU - Lange, Thomas
AU - Heinrichs, Markus
AU - Endres, Dominique
AU - Tebartz van Elst, Ludger
AU - Maier, Simon
TI - Multi-voxel MR-spectroscopy signatures and associations with EEG network hyperexcitability and clinical symptomatology in borderline personality disorder
T2 - Frontiers in psychiatry
J2 - Front Psychiatry
PY - 2026
DA - 2026/
VL - 17
SP - 1708563
SN - 1664-0640
PB - Frontiers Media SA
DO - 10.3389/
UR - https://
LA - en
ER -
CSL-JSON
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{
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{
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{
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{
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{
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{
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},
{
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{
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},
{
"family": "Endres",
"given": "Dominique"
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{
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{
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"given": "Simon"
}
],
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"volume": "17",
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"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
3,
13
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]
}
}
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