t2sv.nii Limited estimated T2* 3D map.
Elizabeth DuPre emdupre
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emdupre
/ nilearn_beta_cneuromod.py
Last active
June 3, 2020 14:01
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| import numpy as np | |
| import pandas as pd | |
| import nibabel as nib | |
| from pathlib import Path, PurePath | |
| from nilearn import image | |
| from numpy.lib import recfunctions | |
| from nilearn.input_data import NiftiMasker | |
| from nistats.first_level_model import FirstLevelModel | |
| """ |
emdupre
/ sub-01_task-movie_run-1_desc-bbregister_bold.svg
Created
October 29, 2019 15:32
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emdupre
/ access_OSF_API.py
Created
April 1, 2019 16:59
Pull download keys for all files listed in an OSF repository
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| import json | |
| import re | |
| import requests | |
| repo = '5hju4' # my example repository, update as appropriate | |
| query = '?filter[name][contains]=confounds_regressors.tsv' # my example query, update or leave blank as appropriate | |
| url = 'https://api.osf.io/v2/nodes/{0}/files/osfstorage/{1}'.format(repo, query) | |
| guids = [] | |
| while True: |
emdupre
/ tedana_outputs_w_3.2.rst
Created
January 11, 2019 14:33
Tedana outputs with version 3.2 of the selection criteria, created by @tsalo
emdupre
/ hypercommented_v3_selcomps.py
Created
November 26, 2018 15:50
Hypercommenting of the v3.2 tedana selection criteria
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| """ | |
| Functions to identify TE-dependent and TE-independent components. | |
| """ | |
| import json | |
| import logging | |
| import pickle | |
| from nilearn._utils import check_niimg | |
| import numpy as np | |
| from scipy import stats |
emdupre
/ group_echos.py
Created
January 8, 2018 17:06
A function to group multi-echo fMRI BOLD sessions, for use in FMRIPREP.
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| import re | |
| from itertools import groupby | |
| multi_echo_ses = {'data': ['sub-01_ses-01_task-view_run-01_echo-1_bold.nii.gz', | |
| 'sub-01_ses-01_task-view_run-01_echo-2_bold.nii.gz', | |
| 'sub-01_ses-01_task-view_run-01_echo-3_bold.nii.gz', | |
| 'sub-01_ses-01_task-view_run-02_echo-1_bold.nii.gz', | |
| 'sub-01_ses-01_task-view_run-02_echo-2_bold.nii.gz', | |
| 'sub-01_ses-01_task-view_run-02_echo-3_bold.nii.gz', | |
| 'sub-01_ses-01_task-rest_run-01_bold.nii.gz', |
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| def create_last_echo_mask(echo_list): | |
| """ | |
| Make a map of longest echo that a voxel can be sampled with, | |
| with minimum value of map as X value of voxel that has median | |
| value in the 1st echo. N.B. larger factor leads to bias to lower TEs | |
| **Inputs** | |
| echo_list | |
| List of file names for all echos of interest |