pcntoolkit

Toolbox for normative modelling and spatial inference of neuroimaging data. https://pcntoolkit.readthedocs.io/en/latest/

https://github.com/amarquand/pcntoolkit

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
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Committers with academic emails
1 of 34 committers (2.9%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (7.8%) to scientific vocabulary

Last synced: 7 months ago · JSON representation ·

Repository

Toolbox for normative modelling and spatial inference of neuroimaging data. https://pcntoolkit.readthedocs.io/en/latest/

Basic Info

Host: GitHub
Owner: amarquand
License: gpl-3.0
Language: Jupyter Notebook
Default Branch: master
Homepage:
Size: 49.7 MB

Statistics

Stars: 139
Watchers: 11
Forks: 55
Open Issues: 18
Releases: 47

Created over 9 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog Contributing License Citation

Predictive Clinical Neuroscience Toolkit

Predictive Clinical Neuroscience software toolkit (formerly nispat).

A Python package for normative modelling, spatial statistics and pattern recognition.

IMPORTANT

Deprecation warning

This is PCNtoolkit version 1.X.X, released originally in June 2025. Any scripts, models, and results created with version 0.X.X are not compatible with this and future versions of the toolkit.

To use the models created with versions 0.35 and earlier, please install the appropriate version using pip install pcntoolkit==0.35, or replace 0.35 with your desired version. The old version of the toolbox is also still available on GitHub.

Installation

bash pip install pcntoolkit

Documentation

See the documentation for more details.

Documentation for the earlier version of the toolbox is available here

Example usage

```python from pcntoolkit import {load_fcon, BLR, NormativeModel}

fcon1000 = load_fcon()

train, test = fcon1000.traintestsplit()

Create a BLR model with heteroskedastic noise

model = NormativeModel(BLR(heteroskedastic=True), inscaler='standardize', outscaler='standardize')

model.fit_predict(train, test) ```

Owner

Name: Andre Marquand
Login: amarquand
Kind: user

Website: http://www.predictiveclinicalneuroscience.com
Repositories: 4
Profile: https://github.com/amarquand

Citation (CITATION.cff)

cff-version: "1.2.0"
message: "If you use this software, please cite it using the metadata below."
title: "PCNtoolkit"
version: "1.0.1"
date-released: "2025-09-04"
doi: "10.5281/zenodo.5207839"
authors:
  - family-names: "Marquand"
    given-names: "Andre"
    orcid: "https://orcid.org/0000-0001-5903-203X"
    affiliation: "Donders Institute for Brain, Cognition, and Behavior"
    affiliation: "Radboud University Medical Center"
    affiliation: "King's College London"
  - family-names: "de Boer"
    given-names: "Stijn"
    orcid: "https://orcid.org/0000-0002-8657-8959"
    affiliation: "Donders Institute for Brain, Cognition and Behaviour"
    affiliation: "Radboud University Medical Center"
  - family-names: "Kia"
    given-names: "Seyed Mostafa"
    orcid: "https://orcid.org/0000-0002-7128-814X"
    affiliation: "Tilburg University"
    affiliation: "Donders Institute for Brain, Cognition, and Behavior"
    affiliation: "University Medical Center Utrecht"
  - family-names: "Rutherford"  
    given-names: "Saige"
    orcid: "https://orcid.org/0000-0003-3006-9044"
    affiliation: "Donders Institute for Brain, Cognition, and Behavior"
    affiliation: "Radboud University Medical Center"
    affiliation: "University of Michigan"
  - family-names: "Fraza"
    given-names: "Charlotte"
    orcid: "https://orcid.org/0000-0002-7088-9250"
    affiliation: "Donders Institute for Brain, Cognition, and Behavior"
    affiliation: "Radboud University Medical Center"
  - family-names: "Rehák Bučková
    given-names: "Barbora"
    orcid: https://orcid.org/0000-0001-5619-3946
    affiliation: "Donders Institute for Brain, Cognition, and Behavior"
    affiliation: "Radboud University Medical Center"
    affiliation: "National Institute of Mental Health: Klecany, CZ"
    affiliation: "Czech Technical University in Prague: Prague, CZ"
    affiliation: "Institute of Computer Science: Prague, CZ"
  - family-names: "Barkema"
    given-names: "Pieter"
    affiliation: "University College London"
    affiliation: "Donders Center for Brain, Cognition, and Behavior"
  - family-names: "Zabihi"
    given-names: "Mariam"
    orcid: "https://orcid.org/0000-0002-7083-2318"
    affiliation: "University College London"
    affiliation: "Donders Institute for Brain, Cognition, and Behavior"
  - family-names: "Dinga" 
    given-names: "Richard"
    orcid: "https://orcid.org/0000-0003-3040-1297"
    affiliation: "Donders Institute for Brain, Cognition and Behaviour"
  - family-names: "Bayer"
    given-names: "Johanna"
    orcid: "https://orcid.org/0000-0003-4891-6256"
    affiliation: "Donders Institute for Brain, Cognition and Behaviour"
  - family-names: "Mennes"
    given-names: "Maarten"
    orcid: "https://orcid.org/0000-0002-7279-3439"
    affiliation: "Donders Institute for Brain, Cognition and Behaviour"
    affiliation: "Radboud University"
    affiliation: "SBGneuro Ltd."
  - family-names: "Huijsdens"
    given-names: "Hester"
    orcid: "https://orcid.org/0000-0001-7039-8390"
    affiliation: "Donders Institute for Brain, Cognition and Behaviour"
  - family-names: "Berthet"
    given-names: "Pierre"
    orcid: "https://orcid.org/0000-0002-6878-6842"
    affiliation: "Donders Institute for Brain, Cognition and Behaviour"
    affiliation: "University of Oslo"
    affiliation: "Stockholm University"
    affiliation: "Universite de Bordeaux"
    affiliation: "Universite Pierre Mendes-France"
    affiliation: "Universite Savoie Mont-Blanc" 

keywords:
  - "normative modeling"
  - "neuroscience"
  - "federated learning"
  - "Bayesian modeling"
  - "software toolkit"
license: "MIT"
repository-code: "https://github.com/amarquand/PCNtoolkit"
url: "https://github.com/andmarquand/PCNtoolkit"
abstract: >
  PCNtoolkit is a lightweight Python package designed to support
  normative modeling workflows in neuroscience.

GitHub Events

Total

Create event: 38
Commit comment event: 2
Issues event: 134
Release event: 23
Watch event: 23
Delete event: 23
Issue comment event: 92
Push event: 221
Pull request event: 44
Fork event: 4

Last Year

Create event: 38
Commit comment event: 2
Issues event: 134
Release event: 23
Watch event: 23
Delete event: 23
Issue comment event: 92
Push event: 221
Pull request event: 44
Fork event: 4

Committers

Last synced: about 3 years ago

All Time

Total Commits: 521
Total Committers: 34
Avg Commits per committer: 15.324
Development Distribution Score (DDS): 0.639

Top Committers

Name	Email	Commits
Seyed Mostafa Kia	m**3@g**m	188
Andre Marquand	a**d@g**m	123
Saige Rutherford	s**r@m**u	40
Thomas Wolfers	t**s@g**m	32
Andre Marquand	a**r@m**l	17
Andre Marquand	a**r@d**l	14
Augub	a**r@g**m	14
Charlotte Fraza	6**a@u**m	10
=	=	10
pierre berthet	b**p@g**m	9
amarquand	a**e@d**l	7
Andre Marquand	a**r@d**l	6
Hester Huijsdens	h**s@g**m	5
amarquand	a**e@M**l	5
Andre Marquand	a**r@d**l	5
amarquand	a**e@I**l	4
Andre Marquand	a**r@d**l	4
Maarten Mennes	m**n@g**m	4
Andre Marquand	a**r@d**l	3
lindenmp	l**s@g**m	3
amarquand	a**e@i**l	2
Sabry Razick	s**r@g**m	2
Andre Marquand	a**r@d**l	2
Andre Marquand	a**r@d**l	2
Andre Marquand	a**r@d**l	1
Andre Marquand	a**r@d**l	1
Andre Marquand	a**r@d**l	1
amarquand	a**e@i**l	1
PBarkema	3**a@u**m	1
Andre Marquand	a**r@d**l	1
and 4 more...

Committer Domains (Top 20 + Academic)

ip-145-116-190-202.wlan-int.ru.nl: 1 dccn-c055.dccn.nl: 1 dccn-c014.dccn.nl: 1 dccn-c047.dccn.nl: 1 ip-145-116-190-193.wlan-int.ru.nl: 1 dccn-c029.dccn.nl: 1 dccn-c025.dccn.nl: 1 dccn-c027.dccn.nl: 1 dccn-c053.dccn.nl: 1 dccn-c042.dccn.nl: 1 ip-145-116-188-33.wlan-int.ru.nl: 1 dccn-c028.dccn.nl: 1 dccn-c026.dccn.nl: 1 dccn-c030.dccn.nl: 1 mpb-andmar.dccn.nl: 1 dccn-c024.dccn.nl: 1 dccn-andmar.dccn.nl: 1 dccn-c032.dccn.nl: 1 mentat004.dccn.nl: 1 med.umich.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 168
Total pull requests: 140
Average time to close issues: about 1 month
Average time to close pull requests: 6 days
Total issue authors: 42
Total pull request authors: 14
Average comments per issue: 1.05
Average comments per pull request: 0.19
Merged pull requests: 114
Bot issues: 0
Bot pull requests: 10

Past Year

Issues: 72
Pull requests: 43
Average time to close issues: 14 days
Average time to close pull requests: 7 days
Issue authors: 8
Pull request authors: 5
Average comments per issue: 0.74
Average comments per pull request: 0.49
Merged pull requests: 28
Bot issues: 0
Bot pull requests: 10

View more stats

Top Authors

Issue Authors

AuguB (96)
likeajumprope (10)
MerveKaptan (6)
alegiac95 (5)
saigerutherford (5)
HSweatman (3)
kkaiwang07 (3)
ymkeverduyn (3)
Sabryr (2)
glick094 (2)
m-petersen (2)
weiwei-wch (1)
adavidBlancoUPF (1)
zzstefan (1)
robertoostenveld (1)

Pull Request Authors

amarquand (88)
AuguB (11)
CharFraza (10)
dependabot[bot] (10)
matei4501 (4)
Hesterhuijsdens (4)
pierreberthet (3)
PBarkema (2)
likeajumprope (2)
ymkeverduyn (2)
Sabryr (1)
saigerutherford (1)
AntoineBernas (1)
bbuckova (1)

Top Labels

Issue Labels

enhancement (12) testing (10) bug (7) development (6) help wanted (5) refactor (3) documentation (2)

Pull Request Labels

dependencies (10) python (6)

Dependencies

doc/requirements.txt pypi

argparse *
bspline *
matplotlib *
nibabel >=2.5.1
numpy >=1.19.5
pandas >=0.25.3
pymc3 >=3.11.2
scipy >=1.3.2
six *
sklearn *
sphinx-automodapi *
sphinx-gallery *
sphinx-tabs *
sphinx_rtd_theme *
torch >=1.1.0

setup.py pypi

argparse *
arviz ==0.11.0
bspline *
matplotlib *
nibabel >=2.5.1
numpy >=1.19.5,<1.23
pandas >=0.25.3
pymc3 >=3.8,<=3.9.3
scipy >=1.3.2
six *
sklearn *
sphinx-tabs *
theano ==1.0.5
torch >=1.1.0

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

pcntoolkit

Science Score: 54.0%

Repository

Basic Info

Statistics

Metadata Files

README.md

Predictive Clinical Neuroscience Toolkit

IMPORTANT

Deprecation warning

Installation

Documentation

Example usage

Create a BLR model with heteroskedastic noise

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies