Code

fMRI demo#242

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HeikoSchuett merged 159 commits intomainrsagroup/rsatoolbox:mainfrom fmri2rsagroup/rsatoolbox:fmri2Copy head branch name to clipboardJul 29, 2024

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Commits

Commits on Sep 17, 2020

• class for parsing derivatives subdirectory in BIDS format

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• added / refined subsetting methods; added function to flatten lists; better __repr__ method

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• added docstrings and function to load SPM beta coefficients optionally using dictionary to subset beta coefficients

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• added option to not provide a dictionary for load_SPM_beta_images()

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Commits on Sep 18, 2020

• np.stack for list of 3d images to 4d array

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• renamed pooling.py to fmri.py

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• inherited class for parsed data of only one subject; methods for loading betas / residuals from SPM output; methods for pooling and saving data as NIfTi and CSV files

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• started coding unit tests

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• fixed __init__ bugs, first parsing unit tests

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• example dataset

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• minor bug fixes and full unit tests for all things pooling

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• CodeFactor fixes

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• CodeFactor fixes

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• starterd coding class to read in 4d nifti files

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Commits on Sep 19, 2020

• added nibabel and pandas to requirements.txt

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Commits on Sep 21, 2020

• Merge branch 'master' into fmri-to-dataset

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Commits on Oct 20, 2020

• Merge branch 'master' into fmri-to-dataset

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Commits on Jun 23, 2021

• merge main

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• updated fmri-tests to folder structure

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Commits on Jun 27, 2021

• fix example data for test_fmri.py

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Commits on Dec 18, 2021

• Merge branch 'main' into fmri-to-dataset

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• stylefix fmri

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• moved fmri to io

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• added init to nifti_filenames

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• style fmri_test

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Commits on Jul 3, 2022

• some notes and a candidate dataset

  

  Jasper van den Bosch

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• somatotopy fmri now separate script

  

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• added standard HRF data file

  

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Commits on Jul 4, 2022

• pct signal change

  

  Jasper van den Bosch

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Commits on Jul 14, 2022

• some notes in fmri demos

  

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Commits on Apr 30, 2023

• Merge branch 'main' into fmri2

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• loading event file for the mur32 study

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Commits on Sep 6, 2023

• mur32 script

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Commits on Sep 10, 2023

• Update fmri_mur32.py

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Commits on Sep 13, 2023

• notes on mur32

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• Merge branch 'main' into fmri-to-dataset

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• Merge branch 'fmri-to-dataset' into fmri2

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• removed heavy data from test package

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Commits on Sep 14, 2023

• split BIDS and SPM related code

  JasperVanDenBosch

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• removed spm methods on bids class

  JasperVanDenBosch

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• updated tests for io.spm

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• some signatures for an fmriprep io interface

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Commits on Sep 15, 2023

• skeleton tests for fmriprep and bids

  JasperVanDenBosch

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• FmriprepRun knows about siblings

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• bids filtering

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• making bids mri files

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• Merge branch 'main' into fmri2

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Commits on Sep 16, 2023

• fmri demo static figures

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• add fmri demo to docs

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• autogen API for new io modules

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• syntax fixes in new module docs

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• access to metadata

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• access events

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• simple standard hrf

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• design matrix utility

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• glm

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• got rid of other potential fmri demo datasets

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Commits on Sep 17, 2023

• fmriprep descriptors

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• loop runs

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• _gen_default_cv_descriptor can deal with list descriptor

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• kernel crash

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• io.fmriprep can provide masks and parcellations

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• demo: subset it

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• parcellation labels

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Commits on Sep 18, 2023

• remove subject 02

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• remove irrelevant conditions

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• define indoor & straight

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• define model rdms

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• simple inference as in eeg demo

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• including bold confounds

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Commits on Sep 19, 2023

• noise

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Commits on Sep 20, 2023

• fewer confounds

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• improved text on demo

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  4746ee9

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• fixed whitespace style issues

  JasperVanDenBosch

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Commits on Oct 13, 2023

• Merge branch 'main' into fmri2

  JasperVanDenBosch

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Commits on Oct 31, 2023

• noise as dataset

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Commits on Nov 3, 2023

• noise ds too large

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• Merge branch 'main' into fmri2

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Commits on Nov 14, 2023

• removed unused neurodataset module and updated docs

  JasperVanDenBosch

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• Merge branch 'main' into fmri2

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• whitespace fixes

  JasperVanDenBosch

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• save memory with smaller datatype for noise

  JasperVanDenBosch

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• axis labels predictor plot

  JasperVanDenBosch

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• better description of DM plot

  JasperVanDenBosch

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Commits on Nov 28, 2023

• small tweaks

  JasperVanDenBosch

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Commits on Mar 2, 2024

• Merge branch 'main' into fmri2

  JasperVanDenBosch

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  3f8bfd4

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• removed unused memory argument

  JasperVanDenBosch

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• can mask fmri data when retrieving it

  JasperVanDenBosch

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• fmri demo: data masked and ROI defined at an earlier stage

  JasperVanDenBosch

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• CI: upgrade cibuildwheel action version

  JasperVanDenBosch

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• added glm image plot to fmri demo

  JasperVanDenBosch

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Commits on Apr 12, 2024

• new fmri demo versions and group IT mask

  JasperVanDenBosch

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Commits on Apr 15, 2024

• nilearn glm

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Commits on Apr 16, 2024

• remove mask gen script

  JasperVanDenBosch

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• unit test for promoting descriptor during Dataset.split_obs

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• dataset promotes split obs descriptor

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• nilearn demo on 3 subjects

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Commits on May 13, 2024

• ensure bids search is predictable

  JasperVanDenBosch

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  6a80822

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• Merge branch 'fmri1' of github.com:JasperVanDenBosch/rsatoolbox into fmri2

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Commits on May 14, 2024

• nilearn demo no max runs

  JasperVanDenBosch

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  5c0d159

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• new statmap start for fmri demo

  JasperVanDenBosch

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  72b2ff2

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• loading statmaps

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Commits on May 26, 2024

• Merge branch 'main' into fmri2

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Commits on Jun 15, 2024

• Merge branch 'main' into fmri2

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Commits on Jun 17, 2024

• SPM example

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• Demo SPM

  jdiedrichsen

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• Cleanup

  jdiedrichsen

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Commits on Jul 4, 2024

• Merge branch 'main' into fmri2

  HeikoSchuett

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Commits on Jul 8, 2024

• Merge branch 'main' into fmri2

  JasperVanDenBosch

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• added nibabel and nitools as optional dependencies

  JasperVanDenBosch

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• SpmGlm uses the io.optional tools to import nitools

  JasperVanDenBosch

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• type annotations for SpmGlm

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• unit test for new SpmGlm class

  JasperVanDenBosch

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  0abe5fd

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• fixed some trailing whitespace

  JasperVanDenBosch

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  4fe4ec4

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• docs fixes

  JasperVanDenBosch

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• style fixes bids

  JasperVanDenBosch

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• style fixes in fmriprep

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Commits on Jul 9, 2024

• bust demo cache

  JasperVanDenBosch

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• fixed paths from spm.mat file

  JasperVanDenBosch

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• re-run spm demo

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• fix os-dependent spm paths

  JasperVanDenBosch

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• forcing posix paths

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• also deal with root

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Commits on Jul 22, 2024

• Merge branch 'main' into fmri2

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  2897bc5

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• restructured the demo overview page

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• moved ignore entries for demo data together

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Commits on Jul 23, 2024

• remove fsl demo template

  JasperVanDenBosch

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• new script for generating rois for mur32

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• glm script

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Commits on Jul 24, 2024

• glm script

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Commits on Jul 25, 2024

• glm script bilateral

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• glm script resids

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• take into account sessions

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• FmriPrepRun makes .ses available

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• unpack statmaps

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• full statmaps demo

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• restricting output data to rois

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Commits on Jul 26, 2024

• glm script: dof and masked resids

  JasperVanDenBosch

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• fixes in glm script

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  3ca5617

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• update with new data structure

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• new test for concat() asserts pattern order

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• re-use code to demote descriptors

  JasperVanDenBosch

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• concat() will reorder patterns where appropriate

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• some style fixes

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• rdm plots

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Commits on Jul 27, 2024

• stylke fix

  JasperVanDenBosch

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• glm script: run-wise mask

  JasperVanDenBosch

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  94ea3d0

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• updated fmri demo names

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  7a3f342

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• move preproc script to demos folder

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• remove roi overlap script

  JasperVanDenBosch

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• patterns demo now in notebook

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  0d22481

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• removed roi def file

  JasperVanDenBosch

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• patterns demo: run inference against fusiform

  JasperVanDenBosch

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  ad4bcc7

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• style fixes in prep script

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  c57866e

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• style fixes

  JasperVanDenBosch

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• patterns demo instructions

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  6d18025

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• explain rois in nilearn demo

  JasperVanDenBosch

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• nilearn demo fixed prec

  JasperVanDenBosch

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• nilearn crossnobis rdm

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