fMRI demo #242

JasperVanDenBosch · 2022-07-04T18:06:34Z

streamlined fMRI access & demo

Demo for RSA on fMRI data in BIDS based on the Mur32 dataset;
BIDS & fMRIprep I/O functionality

resolves calc_rdm_crossnobis indexing shape mismatch #343
resolves fMRI data to pyrsa #89
resolves Dataset.split_obs() should promote target obs_descriptor #328
resolves concat RDMs should ensure conditions are in the same order #346

…better __repr__ method

…y using dictionary to subset beta coefficients

…ing betas / residuals from SPM output; methods for pooling and saving data as NIfTi and CSV files

adkipnis and others added 30 commits September 17, 2020 22:26

class for parsing derivatives subdirectory in BIDS format

9593e8c

added / refined subsetting methods; added function to flatten lists; …

e76ae33

…better __repr__ method

added docstrings and function to load SPM beta coefficients optionall…

de9fd8e

…y using dictionary to subset beta coefficients

added option to not provide a dictionary for load_SPM_beta_images()

4681970

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

2787d8e

renamed pooling.py to fmri.py

ba435b9

inherited class for parsed data of only one subject; methods for load…

f2585cb

…ing betas / residuals from SPM output; methods for pooling and saving data as NIfTi and CSV files

started coding unit tests

f3f49ac

fixed __init__ bugs, first parsing unit tests

d0f8f63

example dataset

3116690

minor bug fixes and full unit tests for all things pooling

f6bb711

CodeFactor fixes

003c342

CodeFactor fixes

56b495c

starterd coding class to read in 4d nifti files

38932dc

added nibabel and pandas to requirements.txt

db58eb8

Merge branch 'master' into fmri-to-dataset

2b23211

Merge branch 'master' into fmri-to-dataset

8ef3a98

merge main

497a51a

updated fmri-tests to folder structure

626eb00

fix example data for test_fmri.py

95a0146

Merge branch 'main' into fmri-to-dataset

5ceceff

stylefix fmri

ae81191

moved fmri to io

6207a97

added init to nifti_filenames

7969629

style fmri_test

ea52543

some notes and a candidate dataset

4d846a9

somatotopy fmri now separate script

fae1150

added standard HRF data file

d070fdd

pct signal change

25e72a2

some notes in fmri demos

3a081ac

JasperVanDenBosch added 28 commits July 25, 2024 15:59

glm script resids

0e557ef

take into account sessions

88c87f7

FmriPrepRun makes .ses available

0ee77a7

unpack statmaps

54ee137

full statmaps demo

506cc75

restricting output data to rois

cbd1319

glm script: dof and masked resids

66380e8

fixes in glm script

3ca5617

update with new data structure

2cad21a

new test for concat() asserts pattern order

83340e2

re-use code to demote descriptors

3f9d20e

concat() will reorder patterns where appropriate

38bcd64

some style fixes

eb9ccc7

rdm plots

ecc05a1

stylke fix

9679d78

glm script: run-wise mask

94ea3d0

updated fmri demo names

7a3f342

move preproc script to demos folder

6932015

remove roi overlap script

e537f56

patterns demo now in notebook

0d22481

removed roi def file

7dc445c

patterns demo: run inference against fusiform

ad4bcc7

style fixes in prep script

c57866e

style fixes

fc3322a

patterns demo instructions

6d18025

explain rois in nilearn demo

94830f2

nilearn demo fixed prec

d4e1e7a

nilearn crossnobis rdm

72dbb09

HeikoSchuett approved these changes Jul 29, 2024

View reviewed changes

HeikoSchuett merged commit 010010e into main Jul 29, 2024
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fMRI demo #242

fMRI demo #242

JasperVanDenBosch commented Jul 4, 2022 •

edited

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fMRI demo #242

fMRI demo #242

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JasperVanDenBosch commented Jul 4, 2022 • edited Loading

streamlined fMRI access & demo

JasperVanDenBosch commented Jul 4, 2022 •

edited

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