148 lines
5.0 KiB
YAML
Executable File
148 lines
5.0 KiB
YAML
Executable File
#################################################
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#
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# Input file for 4D flow
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#
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#################################################
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phase_contrast:
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apply: False
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dealiased: True
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VENC: 400
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meas0: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantom0.9/Mag9AoCo0.90.npz'
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measG: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantom0.9/Mag9AoCo0.9G.npz'
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output: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantom0.9/u_R1.npz'
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resize:
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apply: False
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dim: [120,120,84]
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loadseq: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/Uffine/aoreal.npz'
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save: True
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savepath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/Uffine/aoreal_rs.npz'
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magnetization_CIB:
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apply: False
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loadpath: '/home/yeye/Desktop/PhD/MEDICAL_DATA/Phantom/With_AoCo_9mm/MATLAB_FILES/'
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savepath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantom0.9/Mag9AoCo0.9.npz'
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magnetization:
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apply: False
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loadseq: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/Uffine/aoreal.npz'
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VENC: 250
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save: True
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savepath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/MAG/Mag9AoCoE1.npz'
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sequence:
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apply: false
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checkpoint_path: '/home/yeye/Desktop/Poiseuille/Meas/'
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meshpath: '/home/yeye/Desktop/Poiseuille/Meas/poiseuille.h5'
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sampling_rate: 1
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boxtype: 'fix_resolution'
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#ranges: {'x': [10.8,21] , 'y': [13,19] , 'z': [-0.1,11.5] }
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ranges: {'x': [-1,1] , 'y': [-1,1] , 'z': [0,6] }
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resol: [0.2,0.2,0.2]
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boxsize: [100,100,100]
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name: 'seq'
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cs:
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apply: false
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short: false
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seqpath: '/home/yeye/Desktop/Corrector_2019/Second/Vol3/dicom/u_R1.mat'
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Mpath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/MAG/MG.npz'
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VENC: 160 # cm/s
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noise: false
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R: [2,4,8] # Acceleration factors
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savepath: '/home/yeye/Desktop/Corrector_2019/Second/Vol3/dicom/'
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name: 'ucs'
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kt-BLAST:
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apply: False
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VENC: 3.5 # cm/s
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mode: 'kxky'
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R: [4] # Acceleration factors
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noise: False
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save: True
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savepath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantomRest2E1/'
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name: 'KT_kxky'
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reference:
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apply : False
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#checkpoint_path : '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_ffine/dt0.0005/checkpoint/'
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checkpoint_path : '/home/yeye/Desktop/PhD/AORTA/DATA/undersampling/MAG_2.5/R1/checkpoint/'
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#meshpath : '/home/yeye/Desktop/PhD/AORTA/MESH/aorta_ffine/aorta_ffine_marked.h5'
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meshpath : '/home/yeye/Desktop/PhD/AORTA/MESH/structured/aoreal_2.5_marked.h5'
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under_rate : 1
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fix_const : 0 # 0: false, 1: substract zero_point
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zero_point : [12.79353, 14.32866, 6.51101]
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savepath : '/home/yeye/Desktop/dP/results/MAG_2.5/'
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save : True
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name : 'ref'
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create_checkpoint:
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apply: false
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loadseq: '/home/yeye/Desktop/Corrector_2019/Second/Vol2/dicom/mod/'
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seqname: 'u'
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extension: '.mat'
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mesh_into: '/home/yeye/Desktop/Corrector_2019/Second/Vol2/dicom/mod/aorta.h5'
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boxtype: 'box_zeros'
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boxsize: [80,80,80]
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resol: [0.14,0.14,0.14]
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ranges: {'x': [10.8,21] , 'y': [13,19] , 'z': [-0.1,11.5] }
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masked: False
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masked_seq: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/Uffine/aoreal_2.5.npz'
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dt: 0.0343 #vol 1,2,4
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#dt: 0.03 #vol3
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under_rate: 1
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Rseq: [1]
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savepath: '/home/yeye/Desktop/Corrector_2019/Second/Vol2/dicom/'
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xdmf: true
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change_mesh:
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apply: false
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mode: 'u'
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dt: 0.03
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checkpoint_path: '/home/yeye/Desktop/Poiseuille/Meas/checkpoint/'
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under_rate: 1
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mesh_in: '/home/yeye/Desktop/Poiseuille/Meas/poiseuille.h5'
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mesh_out: '/home/yeye/Desktop/Poiseuille/Meas_leo/poiseuille.h5'
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savepath: '/home/yeye/Desktop/Poiseuille/Meas_leo/'
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xdmf: True
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SENSE:
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apply: False
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R: [2]
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VENC: 250
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Mpath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/MAG/MG.npz'
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savepath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/MAG/MG_sR2.npz'
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create_leo:
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apply: false
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velseq: '/home/yeye/Desktop/Corrector_2019/Meshes/SH3_2.0_R1.npz'
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resol: [0.2,0.2,0.2]
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#ranges: {'x': [-1.2,1.2] , 'y': [-1.2,1.2] , 'z': [-0.2,6.2] }
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ranges: {'x': [10.8,21] , 'y': [13,19] , 'z': [-0.1,11.5] }
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masked: false
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segmentation: '/home/yeye/Desktop/PhD/MEDICAL_DATA/Phantom/With_AoCo_9mm/MATLAB_FILES/Segmented_Aorta.mat'
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outpath: '/home/yeye/Desktop/PhD/PROGRAMS/LEO_matlab/LEO_files/'
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kspace_cib:
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apply : False
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kspace : '/home/yeye/Desktop/Kspaces/9mmRest_2.5/k_space.mat'
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VENC : 320
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output : '/home/yeye/Desktop/FFE_PCA.mat'
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CIBtoH5:
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apply: false
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data_path: '/home/yeye/Desktop/PhD/MEDICAL_DATA/Study_David/Patients/Study_14_GM/velmesh_from_velmat/'
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interpolate: false
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flip: false # Set it True for AoCo = 13mm
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dt: 0.03831417624521074
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mesh_path: '/home/yeye/Desktop/PhD/MEDICAL_DATA/Study_David/Patients/Study_14_GM/velmesh_from_velmat/'
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times: [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27]
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outpath: '/home/yeye/Desktop/Patient_GM/'
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