def main(args):
sys.stdout.flush()
T1 = args.t1
T2 = args.t2
ATLAS = args.atlas
BRAINSFit = args.BRAINSFit
OUTPUT_DIR = args.output
if not os.path.exists(OUTPUT_DIR):
os.makedirs(OUTPUT_DIR)
T2_exists = True
if (T2 == ""):
T2_exists = False
T1_dir = os.path.dirname(T1)
T1_split = os.path.splitext(os.path.basename(T1))
if (T1_split[1] == 'gz'):
T1_base = os.path.splitext(T1_split[0])
else:
T1_base = T1_split[0]
STX_T1 = os.path.join(OUTPUT_DIR, "".join([T1_base, "_stx.nrrd"]))
if (T2_exists):
T2_dir = os.path.dirname(T2)
T2_split = os.path.splitext(os.path.basename(T2))
if (T2_split[1] == 'gz'):
T2_base = os.path.splitext(T2_split[0])
else:
T2_base = T2_split[0]
STX_T2 = os.path.join(OUTPUT_DIR, "".join([T2_base, "_stx.nrrd"]))
if (not os.path.isfile(STX_T1)):
args=[BRAINSFit, '--fixedVolume', ATLAS, '--movingVolume', T1, '--outputVolume', STX_T1, '--useRigid',\
'--initializeTransformMode', 'useCenterOfHeadAlign', '--outputVolumePixelType', 'short']
call_and_print(args)
else:
print_aef("T1 image already aligned")
if (T2_exists):
if (not os.path.isfile(STX_T2)):
args=[BRAINSFit, '--fixedVolume', STX_T1, '--movingVolume', T2, '--outputVolume', STX_T2, '--useRigid',\
'--initializeTransformMode', 'useCenterOfHeadAlign', '--outputVolumePixelType', 'short']
call_and_print(args)
else:
print_aef("T2 image already aligned")
def main(args):
T1 = args.t1
T2 = args.t2
BrainMask = args.mask
output_dir = args.output
ImageMath = args.ImageMath
if not os.path.exists(output_dir):
os.makedirs(output_dir)
if (BrainMask is not None and os.path.exists(BrainMask)):
print("Skull stripping ...")
if (T1 is not None and os.path.exists(T1)):
T1_Base = os.path.splitext(os.path.basename(T1))[0]
T1_STRIPPED = os.path.join(output_dir, T1_Base + "_stripped.nrrd")
args = [ImageMath, T1, '-mask', BrainMask, '-outfile', T1_STRIPPED]
call_and_print(args)
if (T2 is not None and os.path.exists(T2)):
T2_Base = os.path.splitext(os.path.basename(T2))[0]
T2_STRIPPED = os.path.join(output_dir, T2_Base + "_stripped.nrrd")
args = [ImageMath, T2, '-mask', BrainMask, '-outfile', T2_STRIPPED]
call_and_print(args)
else:
print(
"Warning! No brain mask provided or computed. The input T1/T2 will be used in the following steps..."
)
if (T1 is not None and os.path.exists(T1)):
T1_Base = os.path.splitext(os.path.basename(T1))[0]
T1_STRIPPED = os.path.join(output_dir, T1_Base + "_stripped.nrrd")
print("cp ", T1, T1_STRIPPED)
copyfile(T1, T1_STRIPPED)
if (T2 is not None and os.path.exists(T2)):
T2_Base = os.path.splitext(os.path.basename(T2))[0]
T2_STRIPPED = os.path.join(output_dir, T2_Base + "_stripped.nrrd")
print("cp ", T2, T2_STRIPPED)
copyfile(T2, T2_STRIPPED)
def main(args):
T1 = args.t1
T2 = args.t2
ATLAS_DIR = args.at_dir
BRAINSFit = args.BRAINSFit
ANTS = args.ANTS
WarpImageMultiTransform = args.WarpImageMultiTransform
ABC = args.ABC
OUTPUT_DIR = args.output
if not os.path.exists(OUTPUT_DIR):
os.makedirs(OUTPUT_DIR)
PARENT_DIR = os.path.dirname(OUTPUT_DIR)
TEMPLATE = os.path.join(ATLAS_DIR, 'template.mha')
AFFINE_TF = os.path.join(OUTPUT_DIR, 'output_affine_transform.txt')
TEMPLATE_AFF = os.path.join(OUTPUT_DIR, 'template_affine.nrrd')
ANTs_MATRIX_NAME = os.path.join(OUTPUT_DIR, 'template_to_T1_')
ANTs_WARP = ''.join([ANTs_MATRIX_NAME, 'Warp.nii.gz'])
ANTs_INV_WARP = ''.join([ANTs_MATRIX_NAME, 'InverseWarp.nii.gz'])
ANTs_AFFINE = ''.join([ANTs_MATRIX_NAME, 'Affine.txt'])
TEMPLATE_FIN = os.path.join(OUTPUT_DIR, 'template.mha')
if not (os.path.isfile(TEMPLATE) and os.path.isfile(AFFINE_TF)
and os.path.isfile(TEMPLATE_AFF) and os.path.isfile(ANTs_WARP)
and os.path.isfile(ANTs_INV_WARP) and os.path.isfile(ANTs_AFFINE)
and os.path.isfile(TEMPLATE_FIN)):
args = [
BRAINSFit, '--fixedVolume', T1, '--movingVolume', TEMPLATE,
'--outputTransform', AFFINE_TF, '--useRigid',
'--initializeTransformMode', 'useCenterOfHeadAlign'
]
call_and_print(args)
args = [
WarpImageMultiTransform, '3', TEMPLATE, TEMPLATE_AFF, AFFINE_TF,
'-R', T1
]
call_and_print(args)
args = [
ANTS, '3', '-m', 'CC[' + T1 + ',' + TEMPLATE + ',1,4]', '-i',
'100x50x25', '-o', ANTs_MATRIX_NAME, '-t', 'SyN[0.25]', '-r',
'Gauss[3,0]'
]
call_and_print(args)
args = [
WarpImageMultiTransform, '3', TEMPLATE, TEMPLATE_FIN, ANTs_WARP,
ANTs_AFFINE, '-R', T1
]
call_and_print(args)
else:
print_aef('ANTs registration already exists')
for i in range(1, 6):
FILE = os.path.join(ATLAS_DIR, str(i) + '.mha')
FILE_FIN = os.path.join(OUTPUT_DIR, str(i) + '.mha')
if not (os.path.isfile(FILE_FIN)):
args = [
WarpImageMultiTransform, '3', FILE, FILE_FIN, ANTs_WARP,
ANTs_AFFINE, '-R', T1
]
call_and_print(args)
else:
print_aef(FILE_FIN + ' already exist')
segfile_path = os.path.join(PARENT_DIR, 'ABCparam.xml')
segfile = open(segfile_path, 'r')
segfiledata = segfile.read()
segfiledata = segfiledata.replace('@T1_INSEG_IMG@', T1)
segfiledata = segfiledata.replace('@T2_INSEG_IMG@', T2)
segfile = open(segfile_path, 'w')
segfile.write(segfiledata)
segfile.close()
args = [ABC, segfile_path]
call_and_print(args)
def main(args):
T1 = args.t1
T2 = args.t2
ATLAS_DIR = args.at_dir
BRAINSFit = args.BRAINSFit
ANTS = args.ANTS
WarpImageMultiTransform = args.WarpImageMultiTransform
ABC=args.ABC
OUTPUT_DIR = args.output
if not os.path.exists(OUTPUT_DIR):
os.makedirs(OUTPUT_DIR)
PARENT_DIR = os.path.dirname(OUTPUT_DIR)
TEMPLATE = os.path.join(ATLAS_DIR,'template.mha')
AFFINE_TF = os.path.join(OUTPUT_DIR,'output_affine_transform.txt')
TEMPLATE_AFF = os.path.join(OUTPUT_DIR,'template_affine.nrrd')
ANTs_MATRIX_NAME = os.path.join(OUTPUT_DIR,'template_to_T1_')
ANTs_WARP = ''.join([ANTs_MATRIX_NAME,'Warp.nii.gz'])
ANTs_AFFINE = ''.join([ANTs_MATRIX_NAME,'Affine.txt'])
TEMPLATE_FIN = os.path.join(OUTPUT_DIR,'template.mha')
args = [BRAINSFit, '--fixedVolume', T1, '--movingVolume', TEMPLATE, '--outputTransform',AFFINE_TF, '--useRigid', '--initializeTransformMode', 'useCenterOfHeadAlign']
call_and_print(args)
args = [WarpImageMultiTransform, '3', TEMPLATE, TEMPLATE_AFF, AFFINE_TF, '-R', T1]
call_and_print(args)
args = [ANTS, '3', '-m', 'CC['+T1+','+TEMPLATE+',1,4]', '-i', '100x50x25', '-o', ANTs_MATRIX_NAME, '-t', 'SyN[0.25]', '-r', 'Gauss[3,0]']
call_and_print(args)
args = [WarpImageMultiTransform, '3', TEMPLATE, TEMPLATE_FIN, ANTs_WARP, ANTs_AFFINE, '-R', T1]
call_and_print(args)
for i in range(1,6):
FILE = os.path.join(ATLAS_DIR,str(i)+'.mha')
FILE_FIN = os.path.join(OUTPUT_DIR,str(i)+'.mha')
args = [WarpImageMultiTransform, '3', FILE, FILE_FIN, ANTs_WARP, ANTs_AFFINE, '-R', T1]
call_and_print(args)
args = [ABC, os.path.join(PARENT_DIR,'ABCparam.xml')]
call_and_print(args)
def main(args):
sys.stdout.flush()
T1 = args.t1
TEMPLATE_T1_VENTRICLE = args.templateT1Ventricle
TEMPLATE_INV_MASK_VENTRICLE = args.templateInvMaskVentricle
SUBJECT_VENTRICLE_MASK = args.subjectVentricleMask
SUBJECT_TISSUE_SEG = args.subjectTissueSeg
#ANTS REGISTRATION PARAMETERS
REGISTRATION_TYPE = args.registrationType
TRANSFORMATION_STEP = args.transformationStep
ITERATIONS = args.iterations
SIM_METRIC = args.simMetric
SIM_PARAMETER = args.simParameter
GAUSSIAN = args.gaussian
T1_WEIGHT = args.t1Weight
#############################
ImageMath = args.ImageMath
ANTS = args.ANTS
WarpImageMultiTransform = args.WarpImageMultiTransform
OUTPUT_DIR = args.output
if SUBJECT_TISSUE_SEG == "":
tissue_seg = find_file(
".*_labels_EMS.nrrd",
os.path.normpath(os.path.join(OUTPUT_DIR, "..",
"ABC_Segmentation")))
if tissue_seg is not None:
SUBJECT_TISSUE_SEG = tissue_seg
if not os.path.exists(OUTPUT_DIR):
os.makedirs(OUTPUT_DIR)
if (os.path.isfile(TEMPLATE_INV_MASK_VENTRICLE)):
T1_dir = os.path.dirname(T1)
T1_base = os.path.splitext(os.path.basename(T1))[0]
TEMPLATE_INV_MASK_VENTRICLE_base = os.path.splitext(
os.path.basename(TEMPLATE_INV_MASK_VENTRICLE))[0]
TEMPLATE_INV_MASK_VENTRICLE_REG = os.path.join(
OUTPUT_DIR,
"".join([TEMPLATE_INV_MASK_VENTRICLE_base, "_Registered.nrrd"]))
TEMPLATE_T1_VENTRICLE_base = os.path.splitext(
os.path.basename(TEMPLATE_T1_VENTRICLE))[0]
TEMPLATE_T1_VENTRICLE_REG = os.path.join(
OUTPUT_DIR,
"".join([TEMPLATE_T1_VENTRICLE_base, "_Registered.nrrd"]))
SEG_WithoutVent = os.path.join(
OUTPUT_DIR, "".join([T1_base, "_EMS_withoutVent.nrrd"]))
ANTs_MATRIX_NAME = os.path.join(OUTPUT_DIR, T1_base)
ANTs_WARP = os.path.join(OUTPUT_DIR, "".join([T1_base, "Warp.nii.gz"]))
ANTs_INV_WARP = os.path.join(OUTPUT_DIR,
"".join([T1_base, "Warp.nii.gz"]))
ANTs_AFFINE = os.path.join(OUTPUT_DIR, "".join([T1_base,
"Affine.txt"]))
if not (os.path.isfile(ANTs_WARP) and os.path.isfile(ANTs_AFFINE)):
args = [
ANTS, '3', '-m',
SIM_METRIC + '[' + T1 + ',' + TEMPLATE_T1_VENTRICLE + ',' +
T1_WEIGHT + ',' + SIM_PARAMETER + ']', '-i', ITERATIONS, '-o',
ANTs_MATRIX_NAME, '-t', 'SyN[' + TRANSFORMATION_STEP + ']',
'-r', 'Gauss[' + GAUSSIAN + ',0]'
]
call_and_print(args)
else:
print('Ventricle masking : ANTs registration already exists')
args = [
WarpImageMultiTransform, '3', TEMPLATE_INV_MASK_VENTRICLE,
TEMPLATE_INV_MASK_VENTRICLE_REG, ANTs_WARP, ANTs_AFFINE, '-R', T1,
'--use-NN'
]
call_and_print(args)
args = [
WarpImageMultiTransform, '3', TEMPLATE_T1_VENTRICLE,
TEMPLATE_T1_VENTRICLE_REG, ANTs_WARP, ANTs_AFFINE, '-R', T1,
'--use-NN'
]
call_and_print(args)
if SUBJECT_TISSUE_SEG is not None and os.path.exists(
SUBJECT_TISSUE_SEG):
args = [
ImageMath, SUBJECT_TISSUE_SEG, '-mul',
TEMPLATE_INV_MASK_VENTRICLE_REG, '-outfile', SEG_WithoutVent
]
call_and_print(args)
else:
print(
"Template inverse ventricle mask is not a file and cannot be applied"
)
if (os.path.isfile(SUBJECT_VENTRICLE_MASK)
and TEMPLATE_INV_MASK_VENTRICLE == ""):
SUBJECT_VENTRICLE_MASK_base = os.path.splitext(
os.path.basename(SUBJECT_VENTRICLE_MASK))[0]
SUBJECT_VENTRICLE_MASK_INV = os.path.join(
OUTPUT_DIR, SUBJECT_VENTRICLE_MASK_base + '_INV.nrrd')
args = [
ImageMath, SUBJECT_VENTRICLE_MASK, '-threshold', '0,0', '-outfile',
SUBJECT_VENTRICLE_MASK_INV
]
call_and_print(args)
SEG_WithoutVent = os.path.join(
OUTPUT_DIR, "".join([T1_base, "_EMS_withoutVent.nrrd"]))
args = [
ImageMath, SUBJECT_TISSUE_SEG, '-mul', SUBJECT_VENTRICLE_MASK_INV,
'-outfile', SEG_WithoutVent
]
call_and_print(args)
def main(args):
sys.stdout.flush()
T1 = args.t1
ATLAS = args.atlas
#ANTS REGISTRATION PARAMETERS
REGISTRATION_TYPE = args.registrationType
TRANSFORMATION_STEP = args.transformationStep
ITERATIONS = args.iterations
SIM_METRIC = args.simMetric
SIM_PARAMETER = args.simParameter
GAUSSIAN = args.gaussian
T1_WEIGHT = args.t1Weight
#############################
ImageMath = args.ImageMath
ANTS = args.ANTS
WarpImageMultiTransform = args.WarpImageMultiTransform
TISSUE_SEG = args.tissueSeg
VENT_MASK = args.ventricleMask
OUTPUT_DIR = args.output
if not os.path.exists(OUTPUT_DIR):
os.makedirs(OUTPUT_DIR)
AUTO_EACSF_PARENT_DIR = os.path.dirname(
os.path.dirname(os.path.dirname(os.path.dirname(OUTPUT_DIR))))
MASKS_DIR = os.path.join(AUTO_EACSF_PARENT_DIR, 'auto_EACSF/data/masks')
VENT_REGION_MASK = os.path.join(MASKS_DIR, 'vent_region_mask_INV.nrrd')
VENT_MASK_base = os.path.splitext(os.path.basename(VENT_MASK))[0]
VENT_MASK_INV = os.path.join(OUTPUT_DIR, VENT_MASK_base + '_INV.nrrd')
T1_dir = os.path.dirname(T1)
T1_base = os.path.splitext(os.path.basename(T1))[0]
OUT_VENT_MASK = os.path.join(OUTPUT_DIR,
"".join([T1_base, "_AtlasToVent.nrrd"]))
OUT_VENT_REGION_MASK = os.path.join(
OUTPUT_DIR, "".join([T1_base, "_AtlasToVentReg.nrrd"]))
SEG_WithoutVent = os.path.join(OUTPUT_DIR,
"".join([T1_base, "_EMS_withoutVent.nrrd"]))
ANTs_MATRIX_NAME = os.path.join(OUTPUT_DIR, T1_base)
ANTs_WARP = os.path.join(OUTPUT_DIR, "".join([T1_base, "Warp.nii.gz"]))
ANTs_AFFINE = os.path.join(OUTPUT_DIR, "".join([T1_base, "Affine.txt"]))
args = [
ANTS, '3', '-m', SIM_METRIC + '[' + T1 + ',' + ATLAS + ',' +
T1_WEIGHT + ',' + SIM_PARAMETER + ']', '-i', ITERATIONS, '-o',
ANTs_MATRIX_NAME, '-t', 'SyN[' + TRANSFORMATION_STEP + ']', '-r',
'Gauss[' + GAUSSIAN + ',0]'
]
call_and_print(args)
args = [
WarpImageMultiTransform, '3', VENT_REGION_MASK, OUT_VENT_REGION_MASK,
ANTs_WARP, ANTs_AFFINE, '-R', T1, '--use-NN'
]
call_and_print(args)
args = [
ImageMath, TISSUE_SEG, '-mul', OUT_VENT_REGION_MASK, '-outfile',
SEG_WithoutVent
]
call_and_print(args)
if (VENT_MASK != ""):
VM_im = itk.imread(VENT_MASK)
inv_filter = itk.InvertIntensityImageFilter.New(VM_im)
itk.imwrite(inv_filter, VENT_MASK_INV)
args = [
WarpImageMultiTransform, '3', VENT_MASK_INV, OUT_VENT_MASK,
ANTs_WARP, ANTs_AFFINE, '-R', T1, '--use-NN'
]
call_and_print(args)
args = [
ImageMath, SEG_WithoutVent, '-mul', OUT_VENT_MASK, '-outfile',
SEG_WithoutVent
]
call_and_print(args)
def main(args):
T1 = args.t1
T2 = args.t2
T2_exists = True
if (T2 == ""):
T2_exists = False
atlases_dir = args.at_dir
atlases_list = args.at_list
ImageMath = args.ImageMath
FSLBET = args.FSLBET
convertITKformats = args.convertITKformats
ANTS = args.ANTS
WarpImageMultiTransform = args.WarpImageMultiTransform
output_dir = args.output
if not os.path.exists(output_dir):
os.makedirs(output_dir)
atlases_list = atlases_list.split(',')
l = len(atlases_list)
if (l % 2 != 0):
exit('Atlases list : wrong format')
atlases_nb = int(l / 2)
### Convert to *.nii.gz
T1_dir = os.path.dirname(T1)
T1_split = os.path.splitext(os.path.basename(T1))
T1_base = T1_split[0]
if (T1_split[1] != '.gz'):
Input_T1_NII = os.path.join(T1_dir, "".join([T1_base, ".nii.gz"]))
else:
T1_base = os.path.splitext(os.path.basename(T1_base))[0]
Input_T1_NII = T1
args_maj_vote = [ImageMath, Input_T1_NII, '-majorityVoting']
if (T2_exists):
T2_dir = os.path.dirname(T2)
T2_split = os.path.splitext(os.path.basename(T2))
T2_base = T2_split[0]
if (T2_split[1] != '.gz'):
Input_T2_NII = os.path.join(T2_dir, "".join([T2_base, ".nii.gz"]))
else:
T2_base = os.path.splitext(os.path.basename(T2_base))[0]
Input_T2_NII = T2
if (T1 != Input_T1_NII):
args = [convertITKformats, T1, Input_T1_NII]
call_and_print(args)
if (T2_exists):
if (T2 != Input_T2_NII):
args = [convertITKformats, T2, Input_T2_NII]
call_and_print(args)
T1_Only_Mask = os.path.join(T1_dir, "".join([T1_base, "_T1only"]))
if (T2_exists):
T2_Only_Mask = os.path.join(T2_dir, "".join([T2_base, "_T2only"]))
##--> T2 Jointly T1 (FSL BET)
T2_Joint_T1_Mask = os.path.join(
T1_dir, "".join([T1_base, "_T2JointT1_mask.nii.gz"]))
T2_Joint_T1_Mask1 = os.path.join(T1_dir,
"".join([T1_base, "_T2JointT1_tmp1"]))
T2_Joint_T1_Mask2 = os.path.join(T1_dir,
"".join([T1_base, "_T2JointT1_tmp2"]))
args = [
FSLBET, Input_T2_NII, T2_Joint_T1_Mask1, '-f', '0.52', '-g', '0.2',
'-m', '-n', '-A2', Input_T1_NII, '-R'
]
call_and_print(args)
args = [
FSLBET, Input_T2_NII, T2_Joint_T1_Mask2, '-f', '0.52', '-g', '0.2',
'-m', '-n', '-A2', Input_T1_NII, '-R'
]
call_and_print(args)
T2_Joint_T1_Mask1 = ''.join([T2_Joint_T1_Mask1, "_mask.nii.gz"])
T2_Joint_T1_Mask2 = ''.join([T2_Joint_T1_Mask2, "_mask.nii.gz"])
args = [
ImageMath, T2_Joint_T1_Mask1, '-add', T2_Joint_T1_Mask2,
'-outfile', T2_Joint_T1_Mask
]
call_and_print(args)
args = [
ImageMath, T2_Joint_T1_Mask, '-threshold', '1,2', '-outfile',
T2_Joint_T1_Mask
]
call_and_print(args)
args = [
ImageMath, T2_Joint_T1_Mask, '-dilate', '1,1', '-outfile',
T2_Joint_T1_Mask
]
call_and_print(args)
args = [
ImageMath, T2_Joint_T1_Mask, '-erode', '1,1', '-outfile',
T2_Joint_T1_Mask
]
call_and_print(args)
Input_T1_NII_255 = os.path.join(T1_dir, "".join([T1_base, "_255.nii.gz"]))
Pre_SkullMask = os.path.join(T1_dir,
"".join([T1_base, "_255_Skull.nii.gz"]))
args = [
ImageMath, Input_T1_NII, '-rescale', '0,255', '-outfile',
Input_T1_NII_255
]
call_and_print(args)
args = [
ImageMath, Input_T1_NII_255, '-threshold', '0,240', '-outfile',
Pre_SkullMask
]
call_and_print(args)
if (T2_exists):
args = [
ImageMath, T2_Joint_T1_Mask, '-mul', Pre_SkullMask, '-outfile',
T2_Joint_T1_Mask
]
call_and_print(args)
args = [
ImageMath, T2_Joint_T1_Mask, '-erode', '1,1', '-outfile',
T2_Joint_T1_Mask
]
call_and_print(args)
args = [
ImageMath, T2_Joint_T1_Mask, '-dilate', '1,1', '-outfile',
T2_Joint_T1_Mask
]
call_and_print(args)
args = [
ImageMath, T2_Joint_T1_Mask, '-conComp', '1', '-outfile',
T2_Joint_T1_Mask
]
call_and_print(args)
for i in range(0, 2):
args = [
ImageMath, T2_Joint_T1_Mask, '-dilate', '1,1', '-outfile',
T2_Joint_T1_Mask
]
call_and_print(args)
args = [
ImageMath, T2_Joint_T1_Mask, '-erode', '1,1', '-outfile',
T2_Joint_T1_Mask
]
call_and_print(args)
args_maj_vote.append(T2_Joint_T1_Mask)
for k in range(0, atlases_nb):
atlas_base = atlases_list[2 * k]
atlas_type = int(atlases_list[2 * k + 1])
if (atlas_type < 3):
if (atlas_type == 1):
ATLAS_suffix = '_T1.nrrd'
IM_base = T1_base
Input = Input_T1_NII
else:
ATLAS_suffix = '_T2.nrrd'
IM_base = T2_base
Input = Input_T2_NII
ATLAS = os.path.join(atlases_dir,
''.join([atlas_base, ATLAS_suffix]))
ATLAS_MASK = os.path.join(atlases_dir,
''.join([atlas_base, '_brainmask.nrrd']))
OUT_MASK = os.path.join(
output_dir, ''.join([IM_base, '_', atlas_base,
'_mask.nii.gz']))
ANTs_MATRIX_NAME = os.path.join(
output_dir, ''.join([IM_base, '_', atlas_base, '_']))
ANTs_WARP = ''.join([ANTs_MATRIX_NAME, 'Warp.nii.gz'])
ANTs_AFFINE = ''.join([ANTs_MATRIX_NAME, 'Affine.txt'])
args = [
ANTS, '3', '-m', 'CC[' + Input + ',' + ATLAS + ',1,4]', '-i',
'100x50x25', '-o', ANTs_MATRIX_NAME, '-t', 'SyN[0.25]', '-r',
'Gauss[3,0]'
]
else:
T1_ATLAS = os.path.join(atlases_dir,
''.join([atlas_base, '_T1.nrrd']))
T2_ATLAS = os.path.join(atlases_dir,
''.join([atlas_base, '_T2.nrrd']))
ATLAS_MASK = os.path.join(atlases_dir,
''.join([atlas_base, '_brainmask.nrrd']))
OUT_MASK = os.path.join(
output_dir,
''.join([T2_base, '_joined_', atlas_base, '_mask.nii.gz']))
ANTs_MATRIX_NAME = os.path.join(
output_dir, "".join([T2_base, '_joined_', atlas_base, '_']))
ANTs_WARP_ = ''.join([ANTs_MATRIX_NAME, 'Warp.nii.gz'])
ANTs_AFFINE = ''.join([ANTs_MATRIX_NAME, 'Affine.txt'])
args = [
ANTS, '3', '-m',
'CC[' + Input_T1_NII + ',' + T1_ATLAS + ',1,4]', '-m',
'CC[' + Input_T2_NII + ',' + T2_ATLAS + ',1,4]', '-i',
'100x50x25', '-o', ANTs_MATRIX_NAME, '-t', 'SyN[0.25]', '-r',
'Gauss[3,0]'
]
call_and_print(args)
if (atlas_type == 2):
args = [
WarpImageMultiTransform, '3', ATLAS_MASK, OUT_MASK, ANTs_WARP,
ANTs_AFFINE, '-R', Input_T2_NII, '--use-NN'
]
else:
args = [
WarpImageMultiTransform, '3', ATLAS_MASK, OUT_MASK, ANTs_WARP,
ANTs_AFFINE, '-R', Input_T1_NII, '--use-NN'
]
call_and_print(args)
args_maj_vote.append(OUT_MASK)
##--> Majority Vote
Weighted_Majority_Mask = os.path.join(
output_dir, "".join([T1_base, "_weightedMajority.nii.gz"]))
#args=[ImageMath,Input_T1_NII,'-majorityVoting', T2_Joint_T1_Mask, T1_Only_Mask, T2_Only_Mask, COLIN_OUT_MASK, ICMB152_OUT_MASK,
# BIGCSF01_OUT_MASK, BIGCSF02_OUT_MASK,'-outfile', Weighted_Majority_Mask]
args_maj_vote.extend(['-outfile', Weighted_Majority_Mask])
call_and_print(args_maj_vote)
TEMP_ERODE_MASK = os.path.join(output_dir,
"".join([T1_base, "_TEMP_ERODE.nii.gz"]))
args = [
ImageMath, Weighted_Majority_Mask, '-erode', '8,1', '-outfile',
TEMP_ERODE_MASK
]
call_and_print(args)
FINAL_MASK = os.path.join(output_dir,
"".join([T1_base, "_FinalBrainMask.nrrd"]))
args = [
ImageMath, Weighted_Majority_Mask, '-dilate', '1,1', '-outfile',
Weighted_Majority_Mask
]
call_and_print(args)
args = [
ImageMath, Weighted_Majority_Mask, '-erode', '1,1', '-outfile',
FINAL_MASK
]
call_and_print(args)
def main(args):
ABC_TEMPLATE = "<?xml version=\"1.0\"?>\n\
<!DOCTYPE SEGMENTATION-PARAMETERS>\n\
<SEGMENTATION-PARAMETERS>\n\
<SUFFIX>EMS</SUFFIX>\n\
<ATLAS-DIRECTORY>@ATLAS_DIR@</ATLAS-DIRECTORY>\n\
<ATLAS-ORIENTATION>file</ATLAS-ORIENTATION>\n\
<OUTPUT-DIRECTORY>@OUTPUT_DIR@</OUTPUT-DIRECTORY>\n\
<OUTPUT-FORMAT>Nrrd</OUTPUT-FORMAT>\n\
@T1_INSEG_IMG@\
@T2_INSEG_IMG@\
<FILTER-ITERATIONS>10</FILTER-ITERATIONS>\n\
<FILTER-TIME-STEP>0.01</FILTER-TIME-STEP>\n\
<FILTER-METHOD>Curvature flow</FILTER-METHOD>\n\
<MAX-BIAS-DEGREE>4</MAX-BIAS-DEGREE>\n\
@PRIORS@\n\
<INITIAL-DISTRIBUTION-ESTIMATOR>robust</INITIAL-DISTRIBUTION-ESTIMATOR>\n\
<DO-ATLAS-WARP>0</DO-ATLAS-WARP>\n\
<ATLAS-WARP-FLUID-ITERATIONS>50</ATLAS-WARP-FLUID-ITERATIONS>\n\
<ATLAS-WARP-FLUID-MAX-STEP>0.1</ATLAS-WARP-FLUID-MAX-STEP>\n\
<ATLAS-LINEAR-MAP-TYPE>id</ATLAS-LINEAR-MAP-TYPE>\n\
<IMAGE-LINEAR-MAP-TYPE>id</IMAGE-LINEAR-MAP-TYPE>\n\
</SEGMENTATION-PARAMETERS>"
T1 = args.t1
T2 = args.t2
ATLAS_DIR = args.at_dir
BRAINSFit = args.BRAINSFit
ANTS = args.ANTS
WarpImageMultiTransform = args.WarpImageMultiTransform
ABC = args.ABC
OUTPUT_DIR = args.output
OUTPUT_DIR_TISSUE_ATLAS = os.path.join(OUTPUT_DIR,
"TissueSegmentationAtlas")
if not os.path.exists(OUTPUT_DIR):
os.makedirs(OUTPUT_DIR)
if not os.path.exists(OUTPUT_DIR_TISSUE_ATLAS):
os.makedirs(OUTPUT_DIR_TISSUE_ATLAS)
TEMPLATE = os.path.join(ATLAS_DIR, 'template.mha')
AFFINE_TF = os.path.join(OUTPUT_DIR_TISSUE_ATLAS,
'output_affine_transform.txt')
TEMPLATE_AFF = os.path.join(OUTPUT_DIR_TISSUE_ATLAS,
'template_affine.nrrd')
ANTs_MATRIX_NAME = os.path.join(OUTPUT_DIR_TISSUE_ATLAS, 'template_to_T1_')
ANTs_WARP = ''.join([ANTs_MATRIX_NAME, 'Warp.nii.gz'])
ANTs_INV_WARP = ''.join([ANTs_MATRIX_NAME, 'InverseWarp.nii.gz'])
ANTs_AFFINE = ''.join([ANTs_MATRIX_NAME, 'Affine.txt'])
TEMPLATE_FIN = os.path.join(OUTPUT_DIR_TISSUE_ATLAS, 'template.mha')
if not (os.path.isfile(TEMPLATE) and os.path.isfile(AFFINE_TF)
and os.path.isfile(TEMPLATE_AFF) and os.path.isfile(ANTs_WARP)
and os.path.isfile(ANTs_INV_WARP) and os.path.isfile(ANTs_AFFINE)
and os.path.isfile(TEMPLATE_FIN)):
args = [
BRAINSFit, '--fixedVolume', T1, '--movingVolume', TEMPLATE,
'--outputTransform', AFFINE_TF, '--useRigid',
'--initializeTransformMode', 'useCenterOfHeadAlign'
]
call_and_print(args)
args = [
WarpImageMultiTransform, '3', TEMPLATE, TEMPLATE_AFF, AFFINE_TF,
'-R', T1
]
call_and_print(args)
args = [
ANTS, '3', '-m', 'CC[' + T1 + ',' + TEMPLATE + ',1,4]', '-i',
'100x50x25', '-o', ANTs_MATRIX_NAME, '-t', 'SyN[0.25]', '-r',
'Gauss[3,0]'
]
call_and_print(args)
args = [
WarpImageMultiTransform, '3', TEMPLATE, TEMPLATE_FIN, ANTs_WARP,
ANTs_AFFINE, '-R', T1
]
call_and_print(args)
else:
print('ANTs registration already exists')
if os.path.exists(T1):
T1_INSEG_IMG = "<IMAGE>\n\t<FILE>@T1_INSEG_IMG@</FILE>\n\t<ORIENTATION>file</ORIENTATION>\n</IMAGE>\n"
T1_INSEG_IMG = T1_INSEG_IMG.replace("@T1_INSEG_IMG@", T1)
else:
T1_INSEG_IMG = ""
if os.path.exists(T2):
T2_INSEG_IMG = "<IMAGE>\n\t<FILE>@T2_INSEG_IMG@</FILE>\n\t<ORIENTATION>file</ORIENTATION>\n</IMAGE>\n"
T2_INSEG_IMG = T2_INSEG_IMG.replace("@T2_INSEG_IMG@", T2)
else:
T2_INSEG_IMG = ""
predefined_priors = [1.3, 1.0, 0.7, 0.8]
priors_found = find_files("\\d\\.mha", ATLAS_DIR)
for pr_name in priors_found:
FILE_FIN = os.path.join(OUTPUT_DIR_TISSUE_ATLAS,
os.path.basename(pr_name))
if not (os.path.isfile(FILE_FIN)):
args = [
WarpImageMultiTransform, '3', pr_name, FILE_FIN, ANTs_WARP,
ANTs_AFFINE, '-R', T1
]
call_and_print(args)
priors = []
for i in range(len(priors_found) - 1):
if i < len(predefined_priors) - 1:
priors.append(predefined_priors[i])
else:
priors.append(1)
priors.append(predefined_priors[-1])
PRIORS = ""
for pr in priors:
PRIORS += "<PRIOR>" + str(pr) + "</PRIOR>\n"
segfiledata = ABC_TEMPLATE.replace('@T1_INSEG_IMG@', T1_INSEG_IMG)
segfiledata = segfiledata.replace('@T2_INSEG_IMG@', T2_INSEG_IMG)
segfiledata = segfiledata.replace('@ATLAS_DIR@', OUTPUT_DIR_TISSUE_ATLAS)
segfiledata = segfiledata.replace('@PRIORS@', PRIORS)
abc_params = os.path.join(OUTPUT_DIR, 'ABCparam.xml')
segfile = open(abc_params, 'w')
segfile.write(segfiledata)
segfile.close()
labels_out = os.path.join(
OUTPUT_DIR,
os.path.splitext(os.path.basename(T1))[0] + "_labels_EMS.nrrd")
if not (os.path.isfile(labels_out)):
args = [ABC, abc_params]
call_and_print(args)
