def mt_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['mt']['inputs']
label_files = cenc_dirs['mt']['labels']
util.link_inputs( input_files + label_files, link_to_dir )
def prepare( cenc_participant_dir ):
freesurfer_input_dir = os.path.join( cenc_participant_dir, 'freesurfer', 'input' )
util.mkcd_dir( [ freesurfer_input_dir ])
input_files = [ os.path.join( cenc_participant_dir, 'reorient', 't1w.nii.gz'),
os.path.join( cenc_participant_dir, 'reorient', 't2flair.nii.gz'),
os.path.join( cenc_participant_dir, 'reorient', 't2tse.nii.gz')
]
util.link_inputs( input_files, freesurfer_input_dir)
return
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 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')
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)
participant_dir = os.path.abspath(os.path.join(inArgs.cenc_dir, id))
reorient_dir = util.path_relative_to(participant_dir, inArgs.reorient_dir)
wm_lesions_dir = util.path_relative_to(participant_dir, inArgs.out_dir)
wm_lesions_input_dir = os.path.join(wm_lesions_dir, 'input')
wm_lesions_lpa_dir = os.path.join(wm_lesions_dir, '01-lst_lpa')
wm_lesions_lga_dir = os.path.join(wm_lesions_dir, '02-lst_lga')
# Create Output Directory if it doesn't exist
files = [
os.path.abspath(os.path.join(reorient_dir, 't1w.nii.gz')),
os.path.abspath(os.path.join(reorient_dir, 't2flair.nii.gz'))
]
util.mkcd_dir(os.path.join(wm_lesions_input_dir))
util.link_inputs(files, wm_lesions_input_dir)
#
util.mkcd_dir(os.path.join(wm_lesions_lpa_dir), False)
util.mkcd_dir(os.path.join(wm_lesions_lga_dir), True)
util.copy_inputs(files, wm_lesions_lga_dir)
for ii in glob.glob('*.gz'):
os.system('gunzip ' + ii)
util.link_inputs(glob.glob('*.nii'), wm_lesions_lpa_dir)
else:
tarball_filename = id + '_fmri.tar.gz'
if os.path.isfile(os.path.join(out_dir, tarball_filename)):
sys.exit('fMRI tarball already exists for ' + id + '.')
# 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:
affine_out_wras_to_wlps = stage1_output_files[1]
affine_out_wlps_to_wctf = stage1_output_files[3]
fiducials_out_iras = stage1_output_files[2]
fiducials_out_wlps = stage1_output_files[4]
fiducials_out_wctf = stage1_output_files[5]
print stage1_output_files
if inArgs.run and (1 in inArgs.run_stage):
util.print_stage("Entering Stage 1 - Creating matrices", inArgs.verbose)
util.verify_inputs(stage1_input_files, inArgs.verbose)
util.mkcd_dir( stage1_directory )
util.link_inputs( stage1_input_files, stage1_directory)
#
# Save ITK affine matrix
#
if inArgs.verbose:
print
print "Image affine RAS image to RAS world matrix"
print img_affine_matrix_ras
print
util.save_itk_affine_matrix( img_affine_matrix_ras, affine_out_iras_to_wras, inArgs.verbose )
out_fiducials_ctf = util.path_relative_to( stage1_directory, inArgs.out_ctf )
out_fiducials_native = util.path_relative_to( stage1_directory, inArgs.out_native )
out_fiducials_template = util.path_relative_to( stage1_directory, inArgs.out_template )
stage1_input_files = stage0_output_files
stage1_output_files = [ affine_iras_to_wlps, affine_iras_to_wlps, affine_wlps_to_wctf,
out_fiducials_ctf, out_fiducials_native, out_fiducials_template ]
if inArgs.run and (1 in inArgs.run_stage):
util.print_stage('Entering Stage 1 - Calculating affine matrices', inArgs.verbose)
util.verify_inputs(stage1_input_files, inArgs.verbose)
util.mkcd_dir( stage1_directory )
util.link_inputs( stage1_input_files, stage1_directory)
# iCSA to wLPS
util.extract_affine( image_native, affine_iras_to_wlps, True, False, inArgs.verbose)
ctf.icsa_to_wlps( fiducials_native_icsa, inArgs.out_native, affine_iras_to_wlps, inArgs.verbose, inArgs.debug )
# wLPS to wCTF
# When transforming points use the inverse. I have no idea why. Ask ANTs.
ctf.calc_matrix( inArgs.out_native, affine_wlps_to_wctf, 1.0, inArgs.verbose)
ctf.wlps_to_wctf( inArgs.out_native, inArgs.out_ctf, affine_wlps_to_wctf, inArgs.verbose, inArgs.debug)
# wLPS to wTemplate
native_to_template_transform = [ template_to_native[1], template_to_native[0] ]
