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_methods_02_stats( input_dir, verbose=False ):
cenc_dirs = cenc.directories( input_dir )
result_files = [ os.path.join( cenc_dirs['mt']['dirs']['02-stats'], 'magtrans.json') ]
mt_status = util.check_files(result_files, False)
if verbose:
print( cenc_dirs['cenc']['id'] + ', cenc_mt, ' + 'methods_02_stats' + ', ' + str(mt_status) )
return mt_status
def status_prepare( input_dir, 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, False)
if verbose:
print( cenc_dirs['cenc']['id'] + ', cenc_mt, ' + 'prepare' + ', ' + str(mt_status) )
return mt_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_inputs(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, ' + 'input' + ', ' +
str(swi_status))
return swi_status
def results(cenc_participant_id, cenc_participant_dir, cenc_freesurfer_dir,cenc_results_dir, verbose):
util.mkcd_dir( [ cenc_results_dir ], True)
files_to_convert = [ os.path.join( cenc_freesurfer_dir, cenc_participant_id, 'mri', 'nu.mgz'),
os.path.join( cenc_freesurfer_dir, cenc_participant_id, 'mri', 'aseg.mgz'),
os.path.join( cenc_freesurfer_dir, cenc_participant_id, 'mri', 'brainmask.mgz'),
os.path.join( cenc_freesurfer_dir, cenc_participant_id, 'mri', 'aparc.a2009s+aseg.mgz'),
os.path.join( cenc_freesurfer_dir, cenc_participant_id, 'mri', 'wmparc.mgz')
]
# Check if files exist
print files_to_convert
if util.check_files(files_to_convert, True) == False:
sys.exit()
# Create link to directory
freesurfer_results_dir = os.path.abspath(os.path.join( cenc_participant_dir, 'freesurfer','results'))
if not os.path.exists(freesurfer_results_dir):
util.force_symbolic_link( os.path.join( cenc_freesurfer_dir, cenc_participant_id ), freesurfer_results_dir)
# 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_results_dir, 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()
# Create final brain mask.
cenc.create_mask( os.path.join( cenc_results_dir, 'brainmask.nii.gz'),
os.path.join( cenc_results_dir, 'aparc.a2009s+aseg.nii.gz'),
os.path.join( cenc_results_dir, 'mask.nii.gz')
)
# Extract labels for Further processing
cenc_results_labels_dir = os.path.join(cenc_results_dir, 'labels')
util.mkcd_dir( cenc_results_labels_dir, 'labels') )
def results(cenc_participant_id, cenc_participant_dir, cenc_freesurfer_dir,cenc_results_dir, verbose):
util.mkcd_dir( [ cenc_results_dir ], True)
files_to_convert = [ os.path.join( cenc_freesurfer_dir, cenc_participant_id, 'mri', 'nu.mgz'),
os.path.join( cenc_freesurfer_dir, cenc_participant_id, 'mri', 'aseg.mgz'),
os.path.join( cenc_freesurfer_dir, cenc_participant_id, 'mri', 'brainmask.mgz'),
os.path.join( cenc_freesurfer_dir, cenc_participant_id, 'mri', 'aparc.a2009s+aseg.mgz'),
os.path.join( cenc_freesurfer_dir, cenc_participant_id, 'mri', 'wmparc.mgz')
]
# Check if files exist
print files_to_convert
if util.check_files(files_to_convert, True) == False:
sys.exit()
# Create link to directory
freesurfer_results_dir = os.path.abspath(os.path.join( cenc_participant_dir, 'freesurfer','results'))
if not os.path.exists(freesurfer_results_dir):
util.force_symbolic_link( os.path.join( cenc_freesurfer_dir, cenc_participant_id ), freesurfer_results_dir)
# TODO use input node to run this instead of a loop
mc = Node( fs.MRIConvert( out_type = 'niigz'
),
name="mri_convert"
)
mc.iterables = ( "in_file", files_to_convert )
reorient = Node( fsl.Reorient2Std(), name="reorient" )
workflow_convert = Workflow(name='cenc_freesurfer_nipype_workflow')
workflow_convert.base_dir = cenc_results_dir
workflow_convert.connect( [ (mc, reorient, [('out_file', 'in_file')] )]
)
workflow_convert.run()
# Create final brain mask. This takes forever. Speeding it up would be helpful.
cenc.create_mask( os.path.join( cenc_results_dir, 'brainmask.nii.gz'),
os.path.join( cenc_results_dir, 'aparc.a2009s+aseg.nii.gz'),
os.path.join( cenc_results_dir, 'mask.nii.gz')
)
def status_results( input_dir, verbose=False ):
cenc_dirs = cenc.directories( input_dir )
result_files = [ os.path.join( cenc_dirs['mt']['dirs']['results'], 'mt_Affine_nu__mt_m0.nii.gz'),
os.path.join( cenc_dirs['mt']['dirs']['results'], 'mt_Affine_nu__mt_m1.nii.gz'),
os.path.join( cenc_dirs['mt']['dirs']['results'], 'mtr.nii.gz'),
os.path.join( cenc_dirs['mt']['dirs']['results'], 'nu.nii.gz'),
os.path.join( cenc_dirs['results']['dirs']['images'], 'mtr.nii.gz')
]
mt_status = util.check_files(result_files, False)
if verbose:
print( cenc_dirs['cenc']['id'] + ', cenc_mt, ' + 'results' + ', ' + 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['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_results( input_dir, verbose ):
cenc_dirs = cenc.directories( input_dir )
result_files = [ os.path.join( cenc_dirs['results']['dirs']['labels'], 'gm.left_subcortical.nii.gz' ),
os.path.join( cenc_dirs['results']['dirs']['labels'], 'gm.right_subcortical.nii.gz'),
os.path.join( cenc_dirs['results']['dirs']['labels'], 'gm.cerebral_cortex.nii.gz' ),
os.path.join( cenc_dirs['results']['dirs']['labels'], 'gm.cerebellum_cortex.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'], '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_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
util.iw_subprocess( ['cenc_aseg_labels.sh'], True, True, False)
