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)