def swi_link_inputs(swi_info, link_to_dir, change_to_dir=True):
util.mkcd_dir([link_to_dir], change_to_dir)
input_files = swi_info['inputs']
util.link_inputs(input_files + label_files, link_to_dir)
def swi_link_inputs(input_dir, link_to_dir, change_to_dir=True):
cenc_dirs = cenc.directories(input_dir)
util.mkcd_dir([link_to_dir], change_to_dir)
input_files = cenc_dirs['swi']['inputs']
label_files = cenc_dirs['swi']['labels']
util.link_inputs(input_files + label_files, link_to_dir)
def prepare(input_dir):
cenc_dirs = cenc.directories(input_dir)
util.mkcd_dir([cenc_dirs['freesurfer']['input']])
input_files = [
os.path.join(cenc_dirs['cenc']['reorient'], 't1w.nii.gz'),
os.path.join(cenc_dirs['cenc']['reorient'], 't2flair.nii.gz'),
os.path.join(cenc_dirs['cenc']['reorient'], 't2tse.nii.gz')
]
util.link_inputs(input_files, cenc_dirs['freesurfer']['input'])
return
def prepare( input_dir ):
cenc_dirs = cenc.directories( input_dir)
wm_lesions_dir = cenc_dirs['wmlesions']['dirs']['root']
wm_lesions_input_dir = cenc_dirs['wmlesions']['dirs']['input']
wm_lesions_lpa_dir = cenc_dirs['wmlesions']['dirs']['lpa']
# Create Input Directory if it doesn't exist and link files
files = [ os.path.abspath( os.path.join( cenc_dirs['results']['dirs']['images'], 'nu.nii.gz')),
os.path.abspath( os.path.join( cenc_dirs['results']['dirs']['labels'], 'mask.nii.gz')),
os.path.abspath( os.path.join( cenc_dirs['cenc']['reorient'], 't2flair.nii.gz'))
]
util.mkcd_dir( os.path.join( wm_lesions_input_dir ) )
util.link_inputs( files, wm_lesions_input_dir )
def prepare(input_dir):
cenc_dirs = cenc.directories(input_dir)
util.mkcd_dir([cenc_dirs['freesurfer']['input']])
input_files = [os.path.join(cenc_dirs['cenc']['reorient'], 't1w.nii.gz')]
# Preliminary testing of Freesurfer with the T2FLAIR and T2_TSE has not been very successful.
# Removing them from the workflow.
#
# input_files = [ os.path.join( cenc_dirs['cenc']['reorient'], 't2flair.nii.gz'),
# os.path.join( cenc_dirs['cenc']['reorient'], 't2tse.nii.gz')
# ]
util.link_inputs(input_files, cenc_dirs['freesurfer']['input'])
return
def methods_01_register( input_dir, verbose ):
cenc_dirs = cenc.directories( input_dir)
wm_lesions_dir = cenc_dirs['wmlesions']['dirs']['root']
wm_lesions_lpa_dir = cenc_dirs['wmlesions']['dirs']['lpa']
# Register
util.mkcd_dir( [ cenc_dirs['wmlesions']['dirs']['register'] ], True)
files = [ os.path.join( cenc_dirs['wmlesions']['dirs']['input'], 'nu.nii.gz'),
os.path.join( cenc_dirs['wmlesions']['dirs']['input'], 't2flair.nii.gz'),
os.path.join( cenc_dirs['results']['dirs']['labels'], 'mask.nii.gz')
]
util.link_inputs( files, cenc_dirs['wmlesions']['dirs']['register'] )
ants_register('t2flair')
print('\nCENC ID: ' + id)
print('CENC participant directory : ', participant_dir)
print('CENC nifti directory : ', nifti_dir)
print('CENC fMRI tarball : ', os.path.join(out_dir, tarball_filename))
print('\n')
# Create Output Directory if it doesn't exist
files = [
os.path.abspath(os.path.join(dicom_dir, 'dcmConvertAll.cfg')),
os.path.abspath(os.path.join(dicom_dir, 'dcmConvert_cenc.cfg')),
os.path.abspath(os.path.join(nifti_dir, 'rest.nii.gz'))
]
util.mkcd_dir(out_dir)
util.link_inputs(files, out_dir)
files_to_be_tarred = glob.glob('*')
# Create TarBall
tarball = tarfile.open(tarball_filename, 'w:gz')
for f in files_to_be_tarred:
tarball.add(f)
tarball.close()
# Clean Directory
for ii in files_to_be_tarred: