Using NIMADS with NiMARE

How to use the NeuroImaging Meta-Analysis Data Structure (NIMADS) with NiMARE.

from requests import request

from nimare.io import convert_nimads_to_dataset
from nimare.nimads import Studyset

Download Data from NeuroStore

def download_file(url):
    """Download a file from NeuroStore."""
    response = request("GET", url)
    return response.json()


nimads_studyset = download_file("https://neurostore.org/api/studysets/Cv2LLUqG76W9?nested=true")
nimads_annotation = download_file("https://neurostore.org/api/annotations/76PyNqoTNEsE")

Load Data

Load the json files into a NiMADS Studyset object.

studyset = Studyset(nimads_studyset, nimads_annotation)

Convert to NiMARE Dataset

Convert the NiMADS Studyset object to a NiMARE Dataset object. Then you can run NiMARE analyses on the Dataset object.

nimare_dset = studyset.to_dataset()
nimare_dset.coordinates.head()

	id	study_id	contrast_id	x	y	z	space
113	A_PET_study_of_sequential_finger_movements_of_...	A_PET_study_of_sequential_finger_movements_of_...	Sequence-16_vs_Rest,_controls	-10.0	-8.0	56.0	None
111	A_PET_study_of_sequential_finger_movements_of_...	A_PET_study_of_sequential_finger_movements_of_...	Sequence-16_vs_Rest,_controls	16.0	-70.0	44.0	None
112	A_PET_study_of_sequential_finger_movements_of_...	A_PET_study_of_sequential_finger_movements_of_...	Sequence-16_vs_Rest,_controls	32.0	-52.0	44.0	None
114	A_PET_study_of_sequential_finger_movements_of_...	A_PET_study_of_sequential_finger_movements_of_...	Sequence-16_vs_Rest,_controls	18.0	-4.0	56.0	None
115	A_PET_study_of_sequential_finger_movements_of_...	A_PET_study_of_sequential_finger_movements_of_...	Sequence-16_vs_Rest,_controls	-40.0	-32.0	40.0	None

Directly to NiMARE Dataset

Alternatively, you can convert the NiMADS json files directly to a NiMARE Dataset object if you wish to skip using the nimads studyset object directly.

nimare_dset_2 = convert_nimads_to_dataset(nimads_studyset, nimads_annotation)
nimare_dset_2.coordinates.head()

	id	study_id	contrast_id	x	y	z	space
113	A_PET_study_of_sequential_finger_movements_of_...	A_PET_study_of_sequential_finger_movements_of_...	Sequence-16_vs_Rest,_controls	-10.0	-8.0	56.0	None
111	A_PET_study_of_sequential_finger_movements_of_...	A_PET_study_of_sequential_finger_movements_of_...	Sequence-16_vs_Rest,_controls	16.0	-70.0	44.0	None
112	A_PET_study_of_sequential_finger_movements_of_...	A_PET_study_of_sequential_finger_movements_of_...	Sequence-16_vs_Rest,_controls	32.0	-52.0	44.0	None
114	A_PET_study_of_sequential_finger_movements_of_...	A_PET_study_of_sequential_finger_movements_of_...	Sequence-16_vs_Rest,_controls	18.0	-4.0	56.0	None
115	A_PET_study_of_sequential_finger_movements_of_...	A_PET_study_of_sequential_finger_movements_of_...	Sequence-16_vs_Rest,_controls	-40.0	-32.0	40.0	None