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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