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Altered Habenula Resting-State Functional Connectivity and Spatial Associations with Neurotransmitter Receptor Distribution of Major Depressive Disorder with and without Anhedonia.

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  1. [1] § Materials and Methods › fMRI Data Acquisition and Preprocessing › Define ROI ↔ src/seg_hb.py, lines 1 to 33 · score 0.60 · habenula template, Habenula Segmentation, alpha, MNI, volume, Hb · Report a mismatch

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The authors' code

Python · 139 lines · 3.9 KB · MIT · 1 match

  1. #!/usr/bin/env python
  2. # Habenula Segmentation
  3. #
  4. # Arguments:
  5. # T1w
  6. # T2w
  7. #
  8. # Options:
  9. # Myelin
  10. # Hb_center
  11. # Warp_MNI
  12. # OutputBinary
  13. # OutputProb
  14. # Verbose
  15. #
  16. # MinVolume
  17. # T1Min
  18. # T1Max
  19. # T2Min
  20. # T2Max
  21. # Alpha
  22. # NumGrowing
  25. import segment_hb
  26. import argparse
  27. import sys
  28. import os
  29. import subprocess
  31. dirname = os.path.dirname(os.path.realpath(__file__))
  32. hb_template_r = os.path.join(dirname, 'habenula_template_right.nii.gz')
  33. hb_template_l = os.path.join(dirname, 'habenula_template_left.nii.gz')
  35. def run_command(cmd, print_cmd=True):
  36. if print_cmd is True:
  37. print '>> %s' % cmd
  38. p = subprocess.call(cmd, shell=True)
  39. return p
  41. def filename_wo_ext(filename):
  42. if filename[-7:] == '.nii.gz':
  43. return filename[:-7]
  45. elif filename[-4:] == '.nii':
  46. return filename[:-4]
  48. elif filename[-3:] == '.gz':
  49. return filename[:-3]
  51. return filename
  54. parser = argparse.ArgumentParser()
  55. parser.add_argument('-1', dest='t1w', help='T1w image', required=True)
  56. parser.add_argument('-2', dest='t2w', help='T2w image', required=True)
  58. parser.add_argument('-m', dest='myelin', default=None, help='Myelin image')
  60. parser.add_argument('-c', dest='center', default=None, help='Habenula centers')
  61. parser.add_argument('-w', dest='warp_to_acpc', default=None, help='Warp MNI to native')
  62. parser.add_argument('-t', dest='template_threshold', default=0.2, type=float, help='Threshold for warped template')
  64. parser.add_argument('-o', dest='output', default=None, help='Output binary filename')
  66. parser.add_argument('-v', dest='verbose', type=int, default=0)
  67. parser.add_argument('--min_volume', dest='min_volume', type=float, default=100)
  68. parser.add_argument('--t1min', dest='t1min', default=None)
  69. parser.add_argument('--t1max', dest='t1max', default=None)
  70. parser.add_argument('--t2min', dest='t2min', default=10)
  71. parser.add_argument('--t2max', dest='t2max', default=None)
  72. parser.add_argument('--alpha', dest='alpha', type=float, default=0.9)
  73. parser.add_argument('--num_growing', dest='growth', type=int, default=10)
  75. ag = parser.parse_args()
  76. if ag.center is None and ag.warp_to_acpc is None:
  77. sys.stderr.write('Either -c (habenula centers) or -w (warp to native) should be provided.\n')
  78. sys.exit(-1)
  80. if ag.myelin is None:
  81. ag.myelin = filename_wo_ext(os.path.basename(ag.t1w)) + '_div_t2w.nii.gz'
  82. cmd = 'fslmaths %s -div %s %s' % (ag.t1w, ag.t2w, ag.myelin)
  83. run_command(cmd)
  85. if ag.center is None:
  86. ag.center = filename_wo_ext(ag.myelin) + '_habenula_centers_from_template.nii.gz'
  87. tmp = 'tmp_hb_init.nii.gz'
  88. tmp_r = 'tmp_hb_init_r.nii.gz'
  89. tmp_l = 'tmp_hb_init_l.nii.gz'
  91. cmd = 'applywarp -i %s -r %s -o %s -w %s --interp=spline' % (hb_template_r, ag.t1w, tmp, ag.warp_to_acpc)
  92. run_command(cmd)
  93. cmd = 'fslmaths %s -thr %s -bin %s' % (tmp, ag.template_threshold, tmp_r)
  94. run_command(cmd)
  96. cmd = 'applywarp -i %s -r %s -o %s -w %s --interp=spline' % (hb_template_l, ag.t1w, tmp, ag.warp_to_acpc)
  97. run_command(cmd)
  98. cmd = 'fslmaths %s -thr %s -bin %s' % (tmp, ag.template_threshold, tmp_l)
  99. run_command(cmd)
  101. cmd = 'fslmaths %s -mul 2 -add %s %s' % (tmp_l, tmp_r, ag.center)
  102. run_command(cmd)
  104. cmd = 'rm -f %s %s %s' % (tmp, tmp_r, tmp_l)
  105. run_command(cmd)
  107. if ag.output is None:
  108. ag.output = filename_wo_ext(ag.myelin) + '_habenula'
  110. if ag.t1min is not None:
  111. ag.t1min = float(ag.t1min)
  112. if ag.t1max is not None:
  113. ag.t1max = float(ag.t1max)
  114. if ag.t2min is not None:
  115. ag.t2min = float(ag.t2min)
  116. if ag.t2max is not None:
  117. ag.t2max = float(ag.t2max)
  119. #print ag
  120. #sys.exit(0)
  122. return_values = segment_hb.segment_hb(
  123. ag.t1w,
  124. ag.t2w,
  125. ag.myelin,
  126. ag.center,
  127. ag.output,
  128. min_volume=ag.min_volume,
  129. t1min=ag.t1min,
  130. t1max=ag.t1max,
  131. t2min=ag.t2min,
  132. t2max=ag.t2max,
  133. sig_factor=ag.alpha,
  134. growth=ag.growth,
  135. verbose=ag.verbose
  136. )
  138. print '%s %s' % return_values['volumes']

seg_hb.py at commit ce46b50, under MIT · at the source

Overview

Authors: Xiaoyun Luo1, Yanru Wu1, Lijin Yuan1, Yiyun Wang1, Jing Li1, Pu Xu1, Jigang Lian1, Xiaoyan Liu2, Zonglin Shen1,3
ORCID iDs: Lijin Yuan, Yiyun Wang, Xiaoyan Liu, Zonglin Shen
  1. Department of Psychiatry, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
  2. Department of Psychiatry, Affiliated Mental Health Center & Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
  3. Yunnan Clinical Medical Center for Mental Disorders, Kunming, People’s Republic of China
Institutions: Kunming Medical University (China); First Affiliated Hospital of Kunming Medical University (China); Hangzhou Seventh Peoples Hospital (China); Zhejiang University (China)
Journal: Neuropsychiatric disease and treatment, volume 22, article 577735
Dates: received 7 November 2025; accepted 21 March 2026; published online 27 March 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.2147/ndt.s577735 · PMID 41923921 · PMCID PMC13037516 · OpenAlex W7141464315
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: fMRI (modality), human (organism), depression (population), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Connectivity, Statistics, Preprocessing, fMRI & imaging
Keywords: major depressive disorder, anhedonia, habenula, functional connectivity, neurotransmitter receptors
Topic: Functional Brain Connectivity Studies (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Citations: not cited yet (Europe PMC); 53 references in the paper

Abstract

Objective: This study aimed to examine functional connectivity (FC) alterations in patients with major depressive disorder (MDD), specifically comparing those with and without anhedonia.

Methods: 24 MDD patients with anhedonia (MDD-WA), 17 MDD patients without anhedonia (MDD-WoA), and 40 healthy controls (HCs) underwent resting-state functional magnetic resonance imaging (rs-fMRI). Intrinsic brain function was assessed using resting-state FC and spatial associations with neurotransmitter receptor distribution analyses. The habenula (Hb) was selected as the region of interest (ROI), and the whole-brain FC of the Hb was compared across groups. Spatial correlations between inter-group FC differences and whole-brain neurotransmitter receptor/transporter expression templates, derived using the JuSpace tool, were analyzed. Additionally, FC values from differential brain regions were extracted and correlated with the scores on the clinical scale.

Results: Compared to MDD-WoA patients, MDD-WA patients exhibited reduced FC between the Hb and the left middle frontal gyrus (MFG). Enhanced FC was observed between the Hb and bilateral putamen in MDD-WA patients compared to HCs. Additionally, in the MDD-WA group, changes in the Hb whole-brain FC demonstrated positive correlations with the spatial density distribution of specific neurotransmitter receptors and transporters. In contrast, MDD-WoA showed no significant Hb FC differences or neurotransmitter correlations compared to HCs. No significant correlations were found between the FC values of the intergroup-different brain regions and the total SHAPS-C, total HAMD-17, and all HAMD-17 factor scores (anxiety/somatization, weight loss, cognitive disturbance, retardation, and sleep disturbance).

Conclusion: In patients with MDD-WA, FC between the habenula and bilateral putamen, as well as between the habenula and left MFG, was altered. Given that the putamen is a core component of the striatum, all these findings suggest that habenula-prefrontal-striatal dysconnectivity may represent an anhedonia-specific biomarker in MDD. The FC patterns between the habenula and bilateral putamen/left middle frontal gyrus, along with the related neurotransmitter profiles identified in this study, may serve as objective indicators for monitoring therapeutic efficacy in the future.

Reproduced under the paper's license (CC BY-NC), 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.

junqianxulab/habenula_segmentation

License: MIT
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: ce46b504089e419c91f36a738ae6353d735a3653, 2 January 2020
Languages: Python (3)
Size: 10 files, 3 scripts
Software Heritage: archived
Found in: the text, “Define ROI”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NiBabel (1 file), NumPy (1 file), SciPy (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
5 files
At the source: github.com/junqianxulab/habenula_segmentation

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Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 9 authors, 5 keywords, 53 references.

Cite

This paper

Luo, X., Wu, Y., Yuan, L., Wang, Y., Li, J., Xu, P., Lian, J., Liu, X., & Shen, Z. (2026). Altered Habenula Resting-State Functional Connectivity and Spatial Associations with Neurotransmitter Receptor Distribution of Major Depressive Disorder with and without Anhedonia. Neuropsychiatric disease and treatment, 22, 577735. https://doi.org/10.2147/ndt.s577735

BibTeX

@article{luo2026altered,
author = {Luo, Xiaoyun and Wu, Yanru and Yuan, Lijin and Wang, Yiyun and Li, Jing and Xu, Pu and Lian, Jigang and Liu, Xiaoyan and Shen, Zonglin},
title = {{Altered Habenula Resting-State Functional Connectivity and Spatial Associations with Neurotransmitter Receptor Distribution of Major Depressive Disorder with and without Anhedonia}},
journal = {Neuropsychiatric disease and treatment},
year = {2026},
month = mar,
volume = {22},
pages = {577735},
publisher = {Dove Press},
issn = {1176-6328},
doi = {10.2147/ndt.s577735},
url = {https://doi.org/10.2147/ndt.s577735},
pmid = {41923921},
pmcid = {PMC13037516}
}

RIS

TY - JOUR
AU - Luo, Xiaoyun
AU - Wu, Yanru
AU - Yuan, Lijin
AU - Wang, Yiyun
AU - Li, Jing
AU - Xu, Pu
AU - Lian, Jigang
AU - Liu, Xiaoyan
AU - Shen, Zonglin
TI - Altered Habenula Resting-State Functional Connectivity and Spatial Associations with Neurotransmitter Receptor Distribution of Major Depressive Disorder with and without Anhedonia
T2 - Neuropsychiatric disease and treatment
J2 - Neuropsychiatr Dis Treat
PY - 2026
DA - 2026/03/27
VL - 22
SP - 577735
SN - 1176-6328
PB - Dove Press
DO - 10.2147/ndt.s577735
UR - https://doi.org/10.2147/ndt.s577735
LA - en
ER -

CSL-JSON

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"family": "Luo",
"given": "Xiaoyun"
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"issued": {
"date-parts": [
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