Downloading ConWhAt Atlases

Import the fetcher function



In [34]:

    
from conwhat.utils.fetchers import fetch_conwhat_atlas
import glob

Define the output directory



In [ ]:

    
atlas_dir = '/scratch/hpc3230/Data/conwhat_atlases'

Define which atlas to grab



In [4]:

    
atlas_name = 'CWL2k8Sc33Vol3d100s_v01'

Break a leg



In [30]:

    
fetch_conwhat_atlas(atlas_name,atlas_dir,remove_existing=True);









    



removing existing folder


duplicate file detected - removing...
rm CWL2k8Sc33Vol3d100s_v01.zip


downloading data_file CWL2k8Sc33Vol3d100s_v01.zip...
wget https://www.nitrc.org/frs/download.php/10381/CWL2k8Sc33Vol3d100s_v01.zip


unzipping file...
unzip CWL2k8Sc33Vol3d100s_v01.zip


finished unzipping.

The zipped and unzipped atlas folders are now there in the top-level atlas directory;



In [35]:

    
glob.glob(atlas_dir + '/*')









    Out[35]:





['/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01',
 '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01.zip',
 '/scratch/hpc3230/Data/conwhat_atlases/README.md']

The .zip file can be optionally removed automatically if desired.

volumetric atlas folders contain a small number of fairly small .txt files



In [36]:

    
glob.glob('%s/%s/*.txt' %(atlas_dir,atlas_name))









    Out[36]:





['/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/region_mapping_fsav_rh.txt',
 '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/weights.txt',
 '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/mappings.txt',
 '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/region_labels.txt',
 '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/bounding_boxes.txt',
 '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/hemispheres.txt',
 '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/cortex.txt',
 '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/region_mapping_fsav_lh.txt']

...and a larger number of nifti images; one for each atlas structure



In [38]:

    
glob.glob('%s/%s/*.nii.gz' %(atlas_dir,atlas_name))[:5]









    Out[38]:





['/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/vismap_grp_7-64_norm.nii.gz',
 '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/vismap_grp_23-30_norm.nii.gz',
 '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/vismap_grp_65-69_norm.nii.gz',
 '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/vismap_grp_55-70_norm.nii.gz',
 '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/vismap_grp_28-64_norm.nii.gz']



In [39]:

    
len(glob.glob('%s/%s/*.nii.gz' %(atlas_dir,atlas_name)))









    Out[39]:





2445