def status_results(input_dir, verbose):
cenc_dirs = cenc.directories(input_dir)
result_files = [
os.path.join(cenc_dirs['results']['dirs']['labels'],
'gm.cerebral_cortex.nii.gz'),
os.path.join(cenc_dirs['results']['dirs']['labels'],
'gm.cerebellum.nii.gz'),
os.path.join(cenc_dirs['results']['dirs']['labels'],
'wm.cerebral.nii.gz'),
os.path.join(cenc_dirs['results']['dirs']['labels'],
'wm.cerebellum.nii.gz'),
os.path.join(cenc_dirs['results']['dirs']['labels'],
'ventricles.nii.gz'),
os.path.join(cenc_dirs['results']['dirs']['labels'], 'nu.nii.gz'),
os.path.join(cenc_dirs['results']['dirs']['images'], 'nu.nii.gz'),
os.path.join(cenc_dirs['results']['dirs']['images'], 'nu_brain.nii.gz')
]
freesurfer_status_results = util.check_files(result_files, False)
if verbose:
print(cenc_dirs['cenc']['id'] + ', cenc_freesurfer, results, ' +
str(freesurfer_status_results))
return freesurfer_status_results
def status_results( ants_lct_info, verbose=False, debug=False ):
result_files = [ value for key, value in ants_lct_info['results'].items() ]
ants_lct_status = util.check_files(result_files, debug)
if verbose:
print( ants_lct_info['base']['input'] + ', ants_lct, ' + 'results' + ', ' + str(ants_lct_status) )
return ants_lct_status
def status_run(fsinfo, verbose):
result_files = [fsinfo['output']['volume']['wmparc']]
freesurfer_status_run = util.check_files(result_files, False)
if verbose:
print(fsinfo['base']['subject_id'] + ', ' +
fsinfo['base']['subject_dir'] + ', run, ' +
str(freesurfer_status_run))
return freesurfer_status_run
def status_run(input_dir, verbose):
cenc_dirs = cenc.directories(input_dir)
result_files = [os.path.join(cenc_dirs['freesurfer']['mri'], 'wmparc.mgz')]
freesurfer_status_run = util.check_files(result_files, False)
if verbose:
print(cenc_dirs['cenc']['id'] + ', cenc_freesurfer, run, ' +
str(freesurfer_status_run))
return freesurfer_status_run
def status_prepare(input_dir, verbose=False):
cenc_dirs = cenc.directories(input_dir)
input_files = cenc_dirs['swi']['inputs']
label_files = cenc_dirs['swi']['labels']
swi_status = util.check_files(input_files + label_files, False)
if verbose:
print(cenc_dirs['cenc']['id'] + ', cenc_swi, ' + 'prepare' + ', ' +
str(swi_status))
return swi_status
def status_inputs(input_dir, stdout=False, verbose=False):
cenc_dirs = cenc.directories(input_dir)
input_files = cenc_dirs['mt']['inputs']
label_files = cenc_dirs['mt']['labels']
mt_status = util.check_files(input_files + label_files, verbose)
if stdout:
print(cenc_dirs['cenc']['id'] + ', cenc_mt, ' + 'input' + ', ' +
str(mt_status))
return mt_status
def status_methods_02_stats(input_dir, verbose=False):
cenc_dirs = cenc.directories(input_dir)
result_files = [
os.path.join(cenc_dirs['swi']['dirs']['results'], 'magtrans.json')
]
swi_status = util.check_files(result_files, False)
if verbose:
print(cenc_dirs['cenc']['id'] + ', cenc_swi, ' + 'methods_02_stats' +
', ' + str(swi_status))
return swi_status
def status_results(input_dir, verbose=False):
cenc_dirs = cenc.directories( input_dir)
result_files = [ os.path.join( cenc_dirs['wmlesions']['dirs']['results'], 'wmlesions_lpa_t2flair.nii.gz'),
os.path.join( cenc_dirs['wmlesions']['dirs']['results'], 'nu.nii.gz'),
os.path.join( cenc_dirs['wmlesions']['dirs']['results'], 'wmlesions_lpa_pmap.nii.gz'),
os.path.join( cenc_dirs['wmlesions']['dirs']['results'], 'wmlesions_lpa_labels.nii.gz')
]
wmlesions_status = util.check_files(result_files, False)
if verbose:
print( cenc_dirs['cenc']['id'] + ', cenc_wmlesions, results,' + str(wmlesions_status) )
return wmlesions_status
def status_methods_01_register(input_dir, verbose=False):
cenc_dirs = cenc.directories(input_dir)
result_files = [
os.path.join(cenc_dirs['mt']['dirs']['register'],
'mt_Affine_nu__mt_m0_Warped.nii.gz'),
os.path.join(cenc_dirs['mt']['dirs']['register'],
'mt_Affine_nu__mt_m1_Warped.nii.gz'),
os.path.join(cenc_dirs['mt']['dirs']['register'], 'mtr.nii.gz')
]
mt_status = util.check_files(result_files, False)
if verbose:
print(cenc_dirs['cenc']['id'] + ', cenc_mt, ' + 'methods_01_register' +
', ' + str(mt_status))
return mt_status
def status_results(input_dir, verbose=False):
cenc_dirs = cenc.directories(input_dir)
result_files = [
os.path.join(cenc_dirs['swi']['dirs']['results'],
'swi_Affine_nu__swi_m0.nii.gz'),
os.path.join(cenc_dirs['swi']['dirs']['results'],
'swi_Affine_nu__swi_m1.nii.gz'),
os.path.join(cenc_dirs['swi']['dirs']['results'], 'swir.nii.gz'),
os.path.join(cenc_dirs['swi']['dirs']['results'], 'nu.nii.gz'),
os.path.join(cenc_dirs['results']['dirs']['images'], 'swir.nii.gz')
]
swi_status = util.check_files(result_files, False)
if verbose:
print(cenc_dirs['cenc']['id'] + ', cenc_swi, ' + 'results' + ', ' +
str(swi_status))
return swi_status
def status_methods_01_register(config, verbose=False):
input_dir = config['dirs']['input']
cenc_dirs = cenc.directories(input_dir)
result_files = [
os.path.join(cenc_dirs['swi']['dirs']['register'],
'swi_Affine_nu__swi_magnitude.nii.gz'),
os.path.join(cenc_dirs['swi']['dirs']['register'],
'swi_Affine_nu__swi_phase.nii.gz'),
os.path.join(cenc_dirs['swi']['dirs']['register'],
'swi_Affine_nu__swi.nii.gz')
]
swi_status = util.check_files(result_files, False)
if verbose:
print(cenc_dirs['cenc']['id'] + ', cenc_swi, ' +
'methods_01_register' + ', ' + str(swi_status))
return swi_status
def results(input_dir, verbose):
cenc_dirs = cenc.directories(input_dir)
cenc_freesurfer_dir = cenc_dirs['freesurfer']['mri']
util.mkcd_dir([
cenc_dirs['results']['dirs']['root'],
cenc_dirs['results']['dirs']['images'],
cenc_dirs['results']['dirs']['labels']
], True)
files_to_convert = [
os.path.join(cenc_freesurfer_dir, 'nu.mgz'),
os.path.join(cenc_freesurfer_dir, 'aseg.mgz'),
os.path.join(cenc_freesurfer_dir, 'brainmask.mgz'),
os.path.join(cenc_freesurfer_dir, 'aparc.a2009s+aseg.mgz'),
os.path.join(cenc_freesurfer_dir, 'wmparc.mgz')
]
# Check if files exist
if util.check_files(files_to_convert, True) == False:
sys.exit()
# Create link to directory
if not os.path.exists(cenc_dirs['freesurfer']['results']):
util.force_symbolic_link(cenc_dirs['freesurfer']['mri'],
cenc_dirs['freesurfer']['results'])
# TODO use input node to run this instead of a loop. The trick part is to have the files named correctly.
for ii in files_to_convert:
mc = fs.MRIConvert(in_file=ii,
out_file=os.path.join(
cenc_dirs['results']['dirs']['labels'],
str.replace(os.path.basename(ii), '.mgz',
'.nii.gz')),
out_type='niigz')
mc.run()
reorient = fsl.Reorient2Std(in_file=mc.inputs.out_file,
out_file=mc.inputs.out_file)
reorient.run()
# Link nu.nii.gz to results/native/images
result_files = [[
os.path.join(cenc_dirs['results']['dirs']['labels'], 'nu.nii.gz'),
os.path.join(cenc_dirs['results']['dirs']['images'], 'nu.nii.gz')
]]
for ii in result_files:
util.force_hard_link(ii[0], ii[1])
# Create final brain mask.
cenc.create_mask(
os.path.join(cenc_dirs['results']['dirs']['labels'],
'brainmask.nii.gz'),
os.path.join(cenc_dirs['results']['dirs']['labels'],
'aparc.a2009s+aseg.nii.gz'),
os.path.join(cenc_dirs['results']['dirs']['labels'], 'mask.nii.gz'))
# Create macroscopic labels
labels.extract(os.path.join(cenc_dirs['results']['dirs']['labels'],
'aseg.nii.gz'), [],
[10, 11, 12, 13, 17, 18, 49, 50, 51, 52, 53, 54],
os.path.join(cenc_dirs['results']['dirs']['labels'],
'gm.subcortical.nii.gz'),
merge=1)
labels.extract(os.path.join(cenc_dirs['results']['dirs']['labels'],
'aseg.nii.gz'), [], [3, 42],
os.path.join(cenc_dirs['results']['dirs']['labels'],
'gm.cerebral_cortex.nii.gz'),
merge=1)
labels.extract(os.path.join(cenc_dirs['results']['dirs']['labels'],
'aseg.nii.gz'), [], [8, 47],
os.path.join(cenc_dirs['results']['dirs']['labels'],
'gm.cerebellum.nii.gz'),
merge=1)
labels.extract(os.path.join(cenc_dirs['results']['dirs']['labels'],
'aseg.nii.gz'), [], [2, 41],
os.path.join(cenc_dirs['results']['dirs']['labels'],
'wm.cerebral.nii.gz'),
merge=1)
labels.extract(os.path.join(cenc_dirs['results']['dirs']['labels'],
'aseg.nii.gz'), [], [7, 46],
os.path.join(cenc_dirs['results']['dirs']['labels'],
'wm.cerebellum.nii.gz'),
merge=1)
labels.extract(os.path.join(cenc_dirs['results']['dirs']['labels'],
'aseg.nii.gz'), [], [4, 43],
os.path.join(cenc_dirs['results']['dirs']['labels'],
'ventricles.nii.gz'),
merge=1)
# Brain extraction nu.nii.gz
util.iw_subprocess([
'fslmaths',
os.path.join(cenc_dirs['results']['dirs']['images'], 'nu.nii.gz'),
'-mas',
os.path.join(cenc_dirs['results']['dirs']['labels'], 'mask.nii.gz'),
os.path.join(cenc_dirs['results']['dirs']['images'], 'nu_brain.nii.gz')
])
