def get_data(download_folder):
"""get_data
:param download_folder: download destination folder for nifti gz files
:returns brainmaps: list of nii gz images
"""
all_collections = api.get_collections()
collections_with_dois = all_collections[np.logical_not(all_collections.DOI.isnull())]
group_collections = collections_with_dois[collections_with_dois.group_comparison != True]
images = api.get_images(collection_pks=list(group_collections.collection_id))
images = api.filter(df=images, column_name="is_thresholded", field_value=False)
images = api.filter(df=images, column_name="not_mni", field_value=False)
images = api.filter(df=images, column_name="modality", field_value="fMRI-BOLD")
api.download_images(dest_dir=download_folder, images_df=images, resample=False)
return glob("%s/original/*.nii.gz" % (download_folder))
def get_data(download_folder):
'''get_data
:param download_folder: download destination folder for nifti gz files
:returns brainmaps: list of nii gz images
'''
all_collections = api.get_collections()
collections_with_dois = all_collections[np.logical_not(
all_collections.DOI.isnull())]
group_collections = collections_with_dois[
collections_with_dois.group_comparison != True]
images = api.get_images(
collection_pks=list(group_collections.collection_id))
images = api.filter(df=images,
column_name="is_thresholded",
field_value=False)
images = api.filter(df=images, column_name="not_mni", field_value=False)
images = api.filter(df=images,
column_name="modality",
field_value="fMRI-BOLD")
api.download_images(dest_dir=download_folder,
images_df=images,
resample=False)
return glob("%s/original/*.nii.gz" % (download_folder))
from pyneurovault import api import numpy as np all_collections = api.get_collections() collections_with_dois = all_collections[np.logical_not(all_collections.DOI.isnull())] images = api.get_images(collection_pks=list(collections_with_dois.collection_id)) # Remove images that are thresholded images = api.filter(df=images,column_name="is_thresholded",field_value=False) # Not in MNI images = api.filter(df=images,column_name="not_mni",field_value=False) # Just fMRI bold images = api.filter(df=images,column_name="modality",field_value="fMRI-BOLD") # Download all images to file, resample to target outfolder = "/home/vanessa/Documents/Work/NEUROVAULT/mosaic" # If you don't want to resample api.download_images(dest_dir = outfolder,images_df=images,resample=False)
