Mercurial > repos > greg > drmi
changeset 30:6c1fd6d2c07e draft
Uploaded
author | greg |
---|---|
date | Thu, 30 Nov 2017 09:39:31 -0500 |
parents | da507620bd74 |
children | e9bb4e93202a |
files | dmri.py |
diffstat | 1 files changed, 6 insertions(+), 8 deletions(-) [+] |
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--- a/dmri.py Thu Nov 30 09:39:24 2017 -0500 +++ b/dmri.py Thu Nov 30 09:39:31 2017 -0500 @@ -12,6 +12,7 @@ parser = argparse.ArgumentParser() parser.add_argument('--drmi_dataset', dest='drmi_dataset', help='Input dataset') +parser.add_argument('--drmi_dataset_type', dest='drmi_dataset_type', help='Input dataset type') parser.add_argument('--output_nifti1', dest='output_nifti1', help='Output Nifti1 dataset') parser.add_argument('--output_nifti1_extra_files', dest='output_nifti1_extra_files', help='Output Nifti1 extra files') parser.add_argument('--output_png', dest='output_png', help='Output dataset') @@ -34,18 +35,15 @@ # Get input data. input_dir = args.drmi_dataset -if input_dir == 'stanford_hardi': +#if input_dir == 'stanford_hardi': +if args.drmi_dataset_type == "dataset": fetch_stanford_hardi() fdwi = os.path.join(input_dir, 'HARDI150.nii.gz') fbval = os.path.join(input_dir, 'HARDI150.bval') fbvec = os.path.join(input_dir, 'HARDI150.bvec') -elif input_dir == 'sherbrooke_3shell': - fetch_sherbrooke_3shell() - fdwi = os.path.join(input_dir, 'HARDI193.nii.gz') - fbval = os.path.join(input_dir, 'HARDI193.bval') - fbvec = os.path.join(input_dir, 'HARDI193.bvec') -# Load the dMRI datasets. -img = nibabel.load(fdwi) + img = nibabel.load(fdwi) +else: + img, gtab, labels = read_stanford_labels() data = img.get_data() # data is a 4D array where the first 3 dimensions are the i, j, # k voxel coordinates and the last dimension is the number of