Index

_

__init__() (MIR.deformation_regularizer.KL_divergence method) (MIR.image_similarity.NCC method) (MIR.image_similarity.PCC method) (MIR.models.HyperVFA method) (MIR.models.TransMorph method) (MIR.models.TransVFA method) (MIR.models.VFA method)

A

AdvancedDecoder3D (class in MIR.models) AffineReg3D (class in MIR.models) AffineTransformer (class in MIR.models)

apply_affine() (MIR.models.AffineReg3D method) (MIR.models.AffineTransformer method) AverageMeter (class in MIR.utils)

C

calc_J_i() (in module MIR.accuracy_measures) calc_jac_dets() (in module MIR.accuracy_measures) calc_Jstar_1() (in module MIR.accuracy_measures) calc_Jstar_2() (in module MIR.accuracy_measures) calc_measurements() (in module MIR.accuracy_measures) CompRecon (class in MIR.image_similarity) compute_bending_energy() (MIR.deformation_regularizer.DisplacementRegularizer method) compute_gradient_norm() (MIR.deformation_regularizer.DisplacementRegularizer method) Conv3dReLU (class in MIR.models) convex_adam_features() (in module MIR.models) (in module MIR.models.convexAdam) convex_adam_MIND() (in module MIR.models) (in module MIR.models.convexAdam)

convex_adam_MIND_SPR() (in module MIR.models) (in module MIR.models.convexAdam) convex_adam_seg_features() (in module MIR.models) convex_adam_vfa() (in module MIR.models) ConvNeXtSynthHead3D (class in MIR.models) correlation_ratio() (MIR.image_similarity.CorrRatio method) (MIR.image_similarity.LocalCorrRatio method) CorrRatio (class in MIR.image_similarity) create_window() (in module MIR.image_similarity) create_window_3D() (in module MIR.image_similarity) (MIR.image_similarity.NCC_gauss method)

D

Decoder (class in MIR.models) DecoderBlock (class in MIR.models) DefSwinTransformer (class in MIR.models) DefSwinTransformerV2 (class in MIR.models) dice_val_all() (in module MIR.accuracy_measures)

dice_val_substruct() (in module MIR.accuracy_measures) dice_val_VOI() (in module MIR.accuracy_measures) DiceLoss (class in MIR.image_similarity) DiceSegLoss (class in MIR.image_similarity) DisplacementRegularizer (class in MIR.deformation_regularizer) DoubleConv3d (class in MIR.models)

E

EfficientAdvancedSynthHead3D (class in MIR.models)

ensemble_average() (in module MIR.models)

F

FastNCC (class in MIR.image_similarity) fit_warp_to_svf() (in module MIR.models) fit_warp_to_svf_fast() (in module MIR.models) flush() (MIR.utils.Logger method) forward() (MIR.deformation_regularizer.DisplacementRegularizer method) (MIR.deformation_regularizer.Grad2D method) (MIR.deformation_regularizer.Grad3d method) (MIR.deformation_regularizer.Grad3DiTV method) (MIR.deformation_regularizer.GradICON3d method) (MIR.deformation_regularizer.GradICONExact3d method) (MIR.deformation_regularizer.KL_divergence method) (MIR.deformation_regularizer.LocalGrad3d method) (MIR.deformation_regularizer.logBeta method) (MIR.deformation_regularizer.logGaussian method) (MIR.deformation_regularizer.MultiVariateKL_divergence method) (MIR.image_similarity.CompRecon method) (MIR.image_similarity.CorrRatio method) (MIR.image_similarity.DiceLoss method) (MIR.image_similarity.DiceSegLoss method) (MIR.image_similarity.FastNCC method) (MIR.image_similarity.LocalCorrRatio method) (MIR.image_similarity.localMutualInformation method) (MIR.image_similarity.MIND_loss method) (MIR.image_similarity.MutualInformation method) (MIR.image_similarity.NCC method) (MIR.image_similarity.NCC_fp16 method) (MIR.image_similarity.NCC_gauss method) (MIR.image_similarity.NCC_mok method) (MIR.image_similarity.NCC_mok2 method) (MIR.image_similarity.NCC_vfa method) (MIR.image_similarity.NCC_vxm method) (MIR.image_similarity.PCC method) (MIR.image_similarity.SegmentationLoss method) (MIR.image_similarity.SSIM2D method) (MIR.image_similarity.SSIM3D method) (MIR.models.AdvancedDecoder3D method) (MIR.models.AffineReg3D method) (MIR.models.AffineTransformer method) (MIR.models.ConvNeXtSynthHead3D method) (MIR.models.Decoder method) (MIR.models.DecoderBlock method) (MIR.models.DefSwinTransformer method) (MIR.models.DefSwinTransformerV2 method) (MIR.models.DoubleConv3d method) (MIR.models.EfficientAdvancedSynthHead3D method) (MIR.models.GroupNet3D method) (MIR.models.HyperTransMorphTVF method) (MIR.models.HyperTransMorphTVFSPR method) (MIR.models.HyperVFA method) (MIR.models.HyperVFASPR method) (MIR.models.HyperVxmDense method) (MIR.models.MeanStream method) (MIR.models.PreAffineToTemplate method) (MIR.models.SpatialTransformer method) (MIR.models.SSLHead1Lvl method) (MIR.models.SSLHeadNLvl method) (MIR.models.SwinTransformer method) (MIR.models.SynthesisHead3D method) (MIR.models.SynthesisHead3DAdvanced method) (MIR.models.TemplateCreation method) (MIR.models.TransMorph method) (MIR.models.TransMorphAffine method) (MIR.models.TransMorphTVF method) (MIR.models.TransMorphTVFSPR method) (MIR.models.TransVFA method) (MIR.models.VecInt method) (MIR.models.VFA method) (MIR.models.VFASPR method) (MIR.models.VxmDense method) (MIR.models.Warp3d method) (MIR.utils.SpatialTransformer method) (MIR.utils.VecInt method)

G

gaussian() (in module MIR.image_similarity) (MIR.image_similarity.NCC_gauss method) gaussian_kernel() (MIR.image_similarity.CorrRatio method) (MIR.image_similarity.LocalCorrRatio method) get_3DTransMorph3Lvl_config() (in module MIR.models) get_3DTransMorph_config() (in module MIR.models) get_3DTransMorphDWin3Lvl_config() (in module MIR.models) get_3DTransMorphLarge_config() (in module MIR.models) get_3DTransMorphLrn_config() (in module MIR.models) get_3DTransMorphNoConvSkip_config() (in module MIR.models) get_3DTransMorphNoRelativePosEmbd_config() (in module MIR.models) get_3DTransMorphNoSkip_config() (in module MIR.models) get_3DTransMorphNoTransSkip_config() (in module MIR.models) get_3DTransMorphRelativePosEmbdSimple_config() (in module MIR.models) get_3DTransMorphSin_config() (in module MIR.models) get_3DTransMorphSmall_config() (in module MIR.models) get_3DTransMorphTiny_config() (in module MIR.models) get_candidate_from_tensor() (MIR.models.Decoder method)

get_cmap() (in module MIR.utils) get_ConvexAdam_MIND_brain_default_config() (in module MIR.models) get_identity_grid() (in module MIR.accuracy_measures) get_VFA_default_config() (in module MIR.models) get_VXM_1_config() (in module MIR.models) get_VXM_BJ_config() (in module MIR.models) get_VXM_default_config() (in module MIR.models) Grad2D (class in MIR.deformation_regularizer) Grad3d (class in MIR.deformation_regularizer) Grad3DiTV (class in MIR.deformation_regularizer) GradICON3d (class in MIR.deformation_regularizer) GradICONExact3d (class in MIR.deformation_regularizer) gradient_dx() (MIR.deformation_regularizer.DisplacementRegularizer method) gradient_dy() (MIR.deformation_regularizer.DisplacementRegularizer method) gradient_dz() (MIR.deformation_regularizer.DisplacementRegularizer method) gradient_txyz() (MIR.deformation_regularizer.DisplacementRegularizer method) grid_to_flow() (in module MIR.models) GroupNet3D (class in MIR.models)

H

HyperTransMorphTVF (class in MIR.models) HyperTransMorphTVFSPR (class in MIR.models)

HyperVFA (class in MIR.models), [1] HyperVFASPR (class in MIR.models) HyperVxmDense (class in MIR.models)

I

init_weights() (MIR.models.DefSwinTransformer method) (MIR.models.DefSwinTransformerV2 method) (MIR.models.SwinTransformer method)

invert_warp_via_velocity() (in module MIR.models)

K

KL_divergence (class in MIR.deformation_regularizer), [1]

L

ListBatchSampler (class in MIR.models) load_partial_weights() (in module MIR.utils) local_mi() (MIR.image_similarity.localMutualInformation method) LocalCorrRatio (class in MIR.image_similarity)

LocalGrad3d (class in MIR.deformation_regularizer) localMutualInformation (class in MIR.image_similarity) logBeta (class in MIR.deformation_regularizer) logGaussian (class in MIR.deformation_regularizer) Logger (class in MIR.utils)

M

make_affine_from_pixdim() (in module MIR.utils) make_epoch_batches() (in module MIR.models) mean_update() (MIR.models.MeanStream method) MeanStream (class in MIR.models) mi() (MIR.image_similarity.MutualInformation method) MIND_loss (class in MIR.image_similarity) MINDSSC() (MIR.image_similarity.MIND_loss method) MIR.accuracy_measures module, [1] MIR.accuracy_measures.acc_measures module MIR.accuracy_measures.digital_diffeomorphism module MIR.deformation_regularizer module, [1] MIR.deformation_regularizer.GlobalRegularizers module MIR.deformation_regularizer.LocalRegularizers module MIR.image_similarity module, [1] MIR.image_similarity.CompositeRecon module MIR.image_similarity.Correlation_Ratio module MIR.image_similarity.Dice module MIR.image_similarity.MIND_SSC module MIR.image_similarity.Mutual_Information module MIR.image_similarity.Segmentation_Overlap module MIR.image_similarity.SSIM module MIR.models module, [1] MIR.models.affine_reg module MIR.models.atlas_builder module MIR.models.configs_TransMorph module MIR.models.configs_VFA module MIR.models.configs_VoxelMorph module MIR.models.convexAdam module MIR.models.convexAdam.apply_convex module MIR.models.convexAdam.configs_ConvexAdam_MIND module MIR.models.convexAdam.convex_adam_nnUNet module MIR.models.convexAdam.convex_adam_utils module MIR.models.convexAdam.convex_adam_VFA module MIR.models.Deformable_Swin_Transformer module MIR.models.Deformable_Swin_Transformer_v2 module MIR.models.fireants module MIR.models.fireants.interpolator module MIR.models.fireants.io module MIR.models.fireants.losses module MIR.models.fireants.registration module MIR.models.fireants.utils module MIR.models.HyperMorph module MIR.models.HyperTransMorph module MIR.models.MultiMorph module

MIR.models.registration_utils module MIR.models.Segmentation_Heads module MIR.models.Selfsupervised_Learning_Heads module MIR.models.Swin_Transformer module MIR.models.Synthesis_Heads module MIR.models.VoxelMorph module MIR.utils module, [1] MIR.utils.deedsbcv_binary module MIR.utils.other_utils module MIR.utils.registration_utils module MIR.utils.segmentation_utils module MIR.utils.training_utils module MIR.utils.visualization_utils module mk_grid_img() (in module MIR.utils) module MIR.accuracy_measures, [1] MIR.accuracy_measures.acc_measures MIR.accuracy_measures.digital_diffeomorphism MIR.deformation_regularizer, [1] MIR.deformation_regularizer.GlobalRegularizers MIR.deformation_regularizer.LocalRegularizers MIR.image_similarity, [1] MIR.image_similarity.CompositeRecon MIR.image_similarity.Correlation_Ratio MIR.image_similarity.Dice MIR.image_similarity.MIND_SSC MIR.image_similarity.Mutual_Information MIR.image_similarity.Segmentation_Overlap MIR.image_similarity.SSIM MIR.models, [1] MIR.models.affine_reg MIR.models.atlas_builder MIR.models.configs_TransMorph MIR.models.configs_VFA MIR.models.configs_VoxelMorph MIR.models.convexAdam MIR.models.convexAdam.apply_convex MIR.models.convexAdam.configs_ConvexAdam_MIND MIR.models.convexAdam.convex_adam_nnUNet MIR.models.convexAdam.convex_adam_utils MIR.models.convexAdam.convex_adam_VFA MIR.models.Deformable_Swin_Transformer MIR.models.Deformable_Swin_Transformer_v2 MIR.models.fireants MIR.models.fireants.interpolator MIR.models.fireants.io MIR.models.fireants.losses MIR.models.fireants.registration MIR.models.fireants.utils MIR.models.HyperMorph MIR.models.HyperTransMorph MIR.models.MultiMorph MIR.models.registration_utils MIR.models.Segmentation_Heads MIR.models.Selfsupervised_Learning_Heads MIR.models.Swin_Transformer MIR.models.Synthesis_Heads MIR.models.VoxelMorph MIR.utils, [1] MIR.utils.deedsbcv_binary MIR.utils.other_utils MIR.utils.registration_utils MIR.utils.segmentation_utils MIR.utils.training_utils MIR.utils.visualization_utils MultiResPatchSampler3D (class in MIR.utils) MultiVariateKL_divergence (class in MIR.deformation_regularizer) MutualInformation (class in MIR.image_similarity)

N

NCC (class in MIR.image_similarity), [1] NCC_fp16 (class in MIR.image_similarity) NCC_gauss (class in MIR.image_similarity)

NCC_mok (class in MIR.image_similarity) NCC_mok2 (class in MIR.image_similarity) NCC_vfa (class in MIR.image_similarity) NCC_vxm (class in MIR.image_similarity)

O

optimize() (MIR.models.AffineReg3D method)

P

pad_image() (in module MIR.utils) PCC (class in MIR.image_similarity), [1] pcc() (MIR.image_similarity.PCC method)

pdist_squared() (MIR.image_similarity.MIND_loss method) pkload() (in module MIR.utils) PreAffineToTemplate (class in MIR.models)

R

RandomPatchSampler3D (class in MIR.utils) RegistrationHead (class in MIR.models)

resample_to_orginal_space_and_save() (in module MIR.utils) reset() (MIR.utils.AverageMeter method) reset_parameters() (MIR.models.AffineReg3D method)

S

savepkl() (in module MIR.utils) SegmentationLoss (class in MIR.image_similarity) SITReg (in module MIR.models) SLANT_label_reassign() (in module MIR.utils) sliding_window_inference() (in module MIR.utils) softplus() (MIR.models.TransMorphAffine method) SpatialTransformer (class in MIR.models) (class in MIR.utils)

ssim() (in module MIR.image_similarity) SSIM2D (class in MIR.image_similarity) SSIM3D (class in MIR.image_similarity) ssim3D() (in module MIR.image_similarity) SSLHead1Lvl (class in MIR.models) SSLHeadNLvl (class in MIR.models) SwinTransformer (class in MIR.models) SynthesisHead3D (class in MIR.models) SynthesisHead3DAdvanced (class in MIR.models)

T

TemplateCreation (class in MIR.models) to_token() (MIR.models.Decoder method) train() (MIR.models.DefSwinTransformer method) (MIR.models.DefSwinTransformerV2 method) (MIR.models.SwinTransformer method)

TransMorph (class in MIR.models), [1] TransMorphAffine (class in MIR.models) TransMorphTVF (class in MIR.models) TransMorphTVFSPR (class in MIR.models) TransVFA (class in MIR.models), [1]

U

update() (MIR.utils.AverageMeter method)

V

VecInt (class in MIR.models) (class in MIR.utils) VFA (class in MIR.models), [1]

VFASPR (class in MIR.models) vol_bin_centers (MIR.image_similarity.CorrRatio attribute) (MIR.image_similarity.LocalCorrRatio attribute) VxmDense (class in MIR.models)

W

Warp3d (class in MIR.models)

write() (MIR.utils.Logger method) write2csv() (in module MIR.utils)

Z

zoom_img() (in module MIR.utils)