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Bring repo up to date #2

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Commits on Aug 9, 2019

  1. adding conditional tempalte

    @adalca
    adalca committed Aug 9, 2019
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  2. adding link to interactive tipix session

    @adalca
    adalca committed Aug 9, 2019
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Commits on Aug 28, 2019

  1. Update README.md

    @adalca
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Commits on Sep 10, 2019

  1. move to module

    @adalca
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  2. moving files

    @adalca
    adalca committed Sep 10, 2019
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  3. tiny bit of reorg

    @adalca
    adalca committed Sep 10, 2019
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  4. mv register.py

    @adalca
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Commits on Sep 11, 2019

  1. separating layers from networks

    @adalca
    adalca committed Sep 11, 2019
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  2. adding atlas citation

    @adalca
    adalca committed Sep 11, 2019
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  3. Update README.md

    @adalca
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  4. adding deformable templates citation

    @adalca
    adalca committed Sep 11, 2019
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  5. Update README.md

    @adalca
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Commits on Sep 23, 2019

  1. added SLCC loss for SparseVM

    @katiemlewis
    katiemlewis committed Sep 23, 2019
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Commits on Sep 30, 2019

  1. layer cleanup

    @adalca
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Commits on Oct 10, 2019

  1. small losses cleanup

    @adalca
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Commits on Oct 11, 2019

  1. adding atlases to updates

    @adalca
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Commits on Nov 1, 2019

  1. initial reorg and separation of tf/pytorch

    @ahoopes
    ahoopes committed Nov 1, 2019
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  2. fix get_backend()

    @ahoopes
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Commits on Nov 8, 2019

  1. cleanup of networks

    @adalca
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  2. Merge branch 'redesign' of https://github.com/voxelmorph/voxelmorph i… 

    …nto redesign
    @adalca
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  3. adding small Dice fix

    @adalca
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  4. small fix for Dice loss

    @adalca
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  5. Merge branch 'master' of https://github.com/voxelmorph/voxelmorph

    @adalca
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Commits on Nov 9, 2019

  1. Update issue templates

    @voxelmorph
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Commits on Nov 12, 2019

  1. move external packages to in-source

    @ahoopes
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  2. unify generators

    @ahoopes
    ahoopes committed Nov 12, 2019
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  3. update external packages

    @ahoopes
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Commits on Nov 13, 2019

  1. cleanup external package imports for tf backend

    @ahoopes
    ahoopes committed Nov 13, 2019
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  2. add missing layers

    @ahoopes
    ahoopes committed Nov 13, 2019
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  3. cleanup backend imports

    @ahoopes
    ahoopes committed Nov 13, 2019
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  4. cleanup generators

    @ahoopes
    ahoopes committed Nov 13, 2019
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  5. add add_axes flag to load_volfile

    @ahoopes
    ahoopes committed Nov 13, 2019
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  6. Update citations.bib

    @adalca
    adalca committed Nov 13, 2019
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Commits on Nov 15, 2019

  1. unified testing script

    @ahoopes
    ahoopes committed Nov 15, 2019
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  2. cleaned up and generalized the register script

    @ahoopes
    ahoopes committed Nov 15, 2019
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  3. add simple dice function from medipy

    @ahoopes
    ahoopes committed Nov 15, 2019
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Commits on Nov 16, 2019

  1. unify training script

    @ahoopes
    ahoopes committed Nov 16, 2019
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  2. generalize unet

    @ahoopes
    ahoopes committed Nov 16, 2019
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  3. split miccai losses

    @ahoopes
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Commits on Nov 19, 2019

  1. save backend name and rename subdirs

    @ahoopes
    ahoopes committed Nov 19, 2019
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  2. remove unused gitignore

    @ahoopes
    ahoopes committed Nov 19, 2019
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Commits on Nov 25, 2019

  1. add package setup script

    @ahoopes
    ahoopes committed Nov 25, 2019
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  2. add affine support and large-scale cleanup

    @ahoopes
    ahoopes committed Nov 25, 2019
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  3. add pytorch support

    @ahoopes
    ahoopes committed Nov 25, 2019
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  4. bf: make sure to rescale affine

    @ahoopes
    ahoopes committed Nov 25, 2019
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  5. bf: must provide ndims to ResizeTransform layer

    @ahoopes
    ahoopes committed Nov 25, 2019
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  6. merge from master

    @ahoopes
    ahoopes committed Nov 25, 2019
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  7. added some example script documentation

    @ahoopes
    ahoopes committed Nov 25, 2019
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Commits on Jan 17, 2020

  1. add tensorflow scripts dir

    @ahoopes
    ahoopes committed Jan 17, 2020
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  2. replace references to 'subject' with 'scan'

    @ahoopes
    ahoopes committed Jan 17, 2020
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  3. rename generator functions

    @ahoopes
    ahoopes committed Jan 17, 2020
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  4. ideally defer ipython import

    @ahoopes
    ahoopes committed Jan 17, 2020
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Commits on Jan 31, 2020

  1. data/code cleanup

    @ahoopes
    ahoopes committed Jan 31, 2020
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Commits on Feb 4, 2020

  1. added RescaleTransform layer to replace trf_resize()

    @ahoopes
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Commits on Feb 10, 2020

  1. add NMI experimental loss

    @ahoopes
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  2. bf: fix transform rescaling

    @ahoopes
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Commits on Feb 11, 2020

  1. allow for multichannel specification in training scripts

    @ahoopes
    ahoopes committed Feb 11, 2020
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  2. enable multichannel specification on cmdline

    @ahoopes
    ahoopes committed Feb 11, 2020
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  3. use cpu when '--gpu -1' is provided

    @ahoopes
    ahoopes committed Feb 11, 2020
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  4. add instance specific optimization

    @ahoopes
    ahoopes committed Feb 11, 2020
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  5. change instance training default params

    @ahoopes
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Commits on Feb 18, 2020

  1. fix a few IO errors related to multichannel data

    @ahoopes
    ahoopes committed Feb 18, 2020
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  2. fix feature specifications

    @ahoopes
    ahoopes committed Feb 18, 2020
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  3. fix init stats var names

    @ahoopes
    ahoopes committed Feb 18, 2020
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Commits on Feb 21, 2020

  1. adds multi-gpu support to pytorch backend

    @SteffenCzolbe
    SteffenCzolbe committed Feb 21, 2020
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  2. adds model checkpointing support to multi-gpu pytorch models. Save fo… 

    …rmat interchangeable with single gpu/cpu models.
    @SteffenCzolbe
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Commits on Feb 24, 2020

  1. add instance-specific training to networks file

    @ahoopes
    ahoopes committed Feb 24, 2020
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  2. rename to semisupervised

    @ahoopes
    ahoopes committed Feb 24, 2020
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  3. resolved conflict between pytorch cuda device ordering and CUDA_VISIB… 

    …LE_DEVICES environment variable.
    @SteffenCzolbe
    SteffenCzolbe committed Feb 24, 2020
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Commits on Mar 10, 2020

  1. keras --> tf.keras

    adalca committed Mar 10, 2020
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  2. keras --> tf.keras

    adalca committed Mar 10, 2020
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  3. update neuron external package

    @ahoopes
    ahoopes committed Mar 10, 2020
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  4. replace keras with tf.keras

    @ahoopes
    ahoopes committed Mar 10, 2020
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  5. updating from neuron

    @ahoopes
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Commits on Mar 12, 2020

  1. more converting of keras to tf.keras

    @ahoopes
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  2. bf: fix a couple network bugs related to tf.keras updated

    @ahoopes
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Commits on Mar 19, 2020

  1. a few fixes for TF2 support

    @ahoopes
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  2. add hyperparam tuning network

    @ahoopes
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Commits on Mar 20, 2020

  1. add missing unet args for hypernet

    @ahoopes
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  2. add warp compose layer

    @ahoopes
    ahoopes committed Mar 20, 2020
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Commits on Mar 24, 2020

  1. add hypernet training

    @ahoopes
    ahoopes committed Mar 24, 2020
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  2. doc: added some more general training instructions to the readme

    @ahoopes
    ahoopes committed Mar 24, 2020
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Commits on Mar 26, 2020

  1. initial add of surface semi-supervised training

    @ahoopes
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  2. add more surface reg features and a few other fixes

    @ahoopes
    ahoopes committed Mar 26, 2020
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Commits on Mar 31, 2020

  1. add initial (untested) rigid registration option

    @ahoopes
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  2. make EulerToAffine layer

    @ahoopes
    ahoopes committed Mar 31, 2020
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Commits on Apr 1, 2020

  1. bf: optionally add identity to affine in SpatialTransformer

    @ahoopes
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  2. bf: make sure identity is added/not added consistently

    @ahoopes
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Commits on Apr 3, 2020

  1. cleanup affine rigid organization

    @ahoopes
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  2. added the Biweight loss class to implement a robust Tukey Biweight as

    @brf2
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  3. add tukey's biweight loss

    @ahoopes
    ahoopes committed Apr 3, 2020
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Commits on Apr 5, 2020

  1. fixed weight calculation in TukeyBiweight code and added some docs

    @brf2
    brf2 committed Apr 5, 2020
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  2. Merge branch 'redesign' of https://github.com/voxelmorph/voxelmorph i… 

    …nto redesign
    @brf2
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  3. merged TukeyBiweight losses y

    @brf2
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Commits on Apr 6, 2020

  1. use MSE for basic mean-squared losses

    @ahoopes
    ahoopes committed Apr 6, 2020
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  2. allow for bidirectional affine training

    @ahoopes
    ahoopes committed Apr 6, 2020
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Commits on Apr 7, 2020

  1. fix inverse shift and make tf1 compatible

    @ahoopes
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  2. add affine support to ComposeTransform

    @ahoopes
    ahoopes committed Apr 7, 2020
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Commits on Apr 8, 2020

  1. cleanup and remove some things

    @ahoopes
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Commits on Apr 10, 2020

  1. add affine/dense combined network and transform model

    @ahoopes
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Commits on Apr 14, 2020

  1. Train on synthesized image-segmentation pairs.

    @mu40
    mu40 committed Apr 14, 2020
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  2. Unpack warped label maps.

    @mu40
    mu40 committed Apr 14, 2020
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  3. Fix bug in loss term.

    @mu40
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Commits on Apr 15, 2020

  1. Correct default and control model saves.

    @mu40
    mu40 committed Apr 15, 2020
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  2. fix dice loss epsilon

    @ahoopes
    ahoopes committed Apr 15, 2020
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  3. remove transform() function and replace with class

    @ahoopes
    ahoopes committed Apr 15, 2020
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  4. Remove paths.

    @mu40
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Commits on Apr 16, 2020

  1. changed name of VxmCombinedModel to VxmAffineDense, and added some

    @brf2
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Commits on Apr 19, 2020

  1. added some optional parameters to VxmAffineDense to pass to internal

    @brf2
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  2. Assign default input layers.

    @mu40
    mu40 committed Apr 19, 2020
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Commits on Apr 22, 2020

  1. extended rigid case of VxmAffine to support 2D registration

    @brf2
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Commits on Apr 25, 2020

  1. added VxmAffineSegSemiSupervised and modified

    @brf2
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  2. fixed typo and added VxmAffineSurfaceSemiSupervised

    @brf2
    brf2 committed Apr 25, 2020
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  3. minor cleanup

    @adalca
    adalca committed Apr 25, 2020
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  4. Merge branch 'redesign' of https://github.com/voxelmorph/voxelmorph i… 

    …nto redesign
    @adalca
    adalca committed Apr 25, 2020
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  5. rename backends to something simpler

    @ahoopes
    ahoopes committed Apr 25, 2020
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  6. make neuron available directly from tf backend submodule

    @ahoopes
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Commits on Apr 26, 2020

  1. adding name to affine layers

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  2. redesign and upgrade internal unet parameters

    @ahoopes
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  3. remove all models

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  4. update pytorch unet functionality

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  5. merge affine modifications

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  6. adding low init to dense layer in Affine netwrok

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Commits on Apr 27, 2020

  1. Merge pull request #173 from mu40/nf-synth-morph 

    Train on synthesized image-segmentation pairs.
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  2. merge synth seg

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  3. bf: allow for multichannel NCC

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Commits on Apr 28, 2020

  1. fixing affinesemisupervised bug

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  2. Merge branch 'redesign' of https://github.com/voxelmorph/voxelmorph i… 

    …nto redesign
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  3. fixed references.affines in semi-supervised stuff (was returning [0]

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  4. made sure scaling matrix is float in rigid case

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  5. Merge branch 'redesign' of https://github.com/voxelmorph/voxelmorph i… 

    …nto redesign
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  6. adding asserts for affine bug

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  7. Merge branch 'redesign' of https://github.com/voxelmorph/voxelmorph i… 

    …nto redesign
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  8. fixed get_predictor_model method in VxmAffineSegSemiSupervised

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  9. Merge branch 'redesign' of https://github.com/voxelmorph/voxelmorph i… 

    …nto redesign
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  10. fix affine network and add affine composition

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  11. updates to networks that call VxmAffine

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  12. small note

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  13. small merge

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  14. removing blurs limit

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  15. bf: make affine Transform model multi-dimensional

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Commits on Apr 29, 2020

  1. cleaning some extra long lines

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  2. Merge branch 'redesign' of https://github.com/voxelmorph/voxelmorph i… 

    …nto redesign
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Commits on Apr 30, 2020

  1. adding rescale_affine support

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Commits on May 1, 2020

  1. fixed affine init in Transform

    @brf2
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  2. fix a few redesign issues

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Commits on May 4, 2020

  1. large-scale redesign and bugfixes

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  2. merge from upstream

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Commits on May 5, 2020

  1. a few pytorch network and training fixes

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  2. fix up affines in registration script

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  3. merge Malte's updates

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  4. Merge pull request #153 from SteffenCzolbe/multi_gpu_support_pytorch 

    Multi-gpu support for pytorch
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Commits on May 11, 2020

  1. fix pytorch model-size and training slowness

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Commits on May 25, 2020

  1. changing grad loss to be row wise

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  2. changing ncc loss to be row wise

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  3. changing grad loss to be row wise

    @adalca
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Commits on Jun 3, 2020

  1. squeeze data when loading from nibabel

    @ahoopes
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  2. add bidir training option to VxmAffineDense model

    @ahoopes
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  3. rename script subdirs

    @ahoopes
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  4. merge from upstream

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Commits on Jun 6, 2020

  1. fixed bidir=True case in VxmAffineDense, added a function to compute a

    @brf2
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Commits on Jun 9, 2020

  1. moved import of neuron sandbox into interior of Grad class init with a

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  2. moved sandbox imports.

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Commits on Jun 19, 2020

  1. nf: add robust GaussianBlur layer

    @ahoopes
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  2. bf: make sure dense layer is scaled during rigid registration

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Commits on Jun 20, 2020

  1. nf: revert previous rescale behaviour and support [translation, linea… 

    …r] component rescale
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  2. merge from upstream

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  3. bf: add deleted tf losses file

    @ahoopes
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Commits on Jun 22, 2020

  1. small cleanup

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  2. local params

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  3. bf: replace K.ones with tf.ones

    @ahoopes
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  4. added multi-channel support to VxmAffineDense

    @brf2
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Commits on Jun 23, 2020

  1. update neuron

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  2. Merge branch 'redesign' of https://github.com/voxelmorph/voxelmorph i… 

    …nto redesign
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Commits on Jul 29, 2020

  1. nf: add input shape support for unet

    @ahoopes
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  2. bug fix: grab correct shape from image in apply_transform()

    @ahoopes
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Commits on Aug 3, 2020

  1. cleanup a few TF scripts

    @ahoopes
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  2. add half-res decoder option and use maxpooling in unet

    @ahoopes
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  3. temporarily remove troublesome affine code for redesign merge

    @ahoopes
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  4. scale gradient loss by downsize factor

    @ahoopes
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  5. cleanup script doc

    @ahoopes
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  6. remove neuron from vxm distribution

    @ahoopes
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  7. bf: allow for null GPU in device config

    @ahoopes
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  8. add legacy branch note to readme

    @ahoopes
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  9. touch up readme example commands

    @ahoopes
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Commits on Aug 5, 2020

  1. keepdims title

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  2. adding fill value

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Commits on Aug 6, 2020

  1. cleanup of imports

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  2. adding spatial transfomer to vxm layers

    @adalca
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  3. cleanup networks

    @adalca
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  4. cleanup of utils

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Commits on Aug 7, 2020

  1. adding util

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  2. affine to shift fix

    @adalca
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  3. adding ne.utils calls

    @adalca
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  4. remove unused package requirements from setup.py

    @ahoopes
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  5. some description cleanup, though plenty left to do

    @adalca
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  6. include SynthSeg as a direct submodule

    @ahoopes
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  7. remove bold citations

    @ahoopes
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Commits on Aug 8, 2020

  1. cleanup instance training

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  2. Merge branch 'master' of https://github.com/voxelmorph/voxelmorph

    @ahoopes
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  3. switch neuron to neurite

    @ahoopes
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  4. use local VecInt layer

    @ahoopes
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  5. moving zoom to neurite

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  6. Merge branch 'master' of https://github.com/voxelmorph/voxelmorph

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Commits on Aug 9, 2020

  1. fix resize import

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Commits on Aug 12, 2020

  1. remove gradient loss blurring for now

    @ahoopes
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  2. fixes for PEP8 compliance

    @ahoopes
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Commits on Aug 13, 2020

  1. Fix NCC class in torch/losses.py

    Paul Weinmann committed Aug 13, 2020
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Commits on Aug 14, 2020

  1. fixed syntax errors

    @ahoopes
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  2. add get_config to RescaleTransform

    @ahoopes
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  3. fixing utils

    @adalca
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  4. adding max pool options

    @adalca
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  5. Merge branch 'master' of https://github.com/voxelmorph/voxelmorph

    @adalca
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Commits on Aug 17, 2020

  1. remove return in unet __init__

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Commits on Aug 19, 2020

  1. pep8

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Commits on Aug 21, 2020

  1. Merge pull request #212 from p-wein/master 

    Fixes #211 NCC class in torch/losses.py
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Commits on Aug 26, 2020

  1. supporting residual

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  2. Merge branch 'master' of https://github.com/voxelmorph/voxelmorph

    @adalca
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Commits on Sep 3, 2020

  1. update setup.py

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Commits on Sep 5, 2020

  1. adding optional name to unet

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Commits on Sep 7, 2020

  1. bf: output flow prob params when use_probs is enabled

    @ahoopes
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  2. bf: fix parser namespace typo

    @ahoopes
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  3. bf: use Transform model for registration script

    @ahoopes
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  4. expand instance-training capabilities

    @ahoopes
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  5. rename semisupervised training scripts

    @ahoopes
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  6. rename semisupervised surf to pointcloud

    @ahoopes
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  7. bf: adapt synthseg for neurite changes

    @ahoopes
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  8. rename unsupervised seg scripts

    @ahoopes
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  9. bf: cache missing inshape and nb_feats

    @ahoopes
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Commits on Sep 10, 2020

  1. adding jacobian_determinant utility

    @adalca
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Commits on Sep 12, 2020

  1. bf: fix for tf1/2 Dice loss compat

    @ahoopes
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  2. nf: add pytorch dice loss

    @ahoopes
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  3. bf: make sure torch dice has no div by zero

    @ahoopes
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Commits on Sep 14, 2020

  1. fixing tf 2.0 div no nan

    @adalca
    adalca committed Sep 14, 2020
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  2. merge fix

    @adalca
    adalca committed Sep 14, 2020
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Commits on Sep 16, 2020

  1. use model name as layer name prefix for Unet and VxmDense

    @ahoopes
    ahoopes committed Sep 16, 2020
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Commits on Sep 19, 2020

  1. bf: fix rescale-computed warp shape for Transform network

    @ahoopes
    ahoopes committed Sep 19, 2020
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  2. add checks for backend package

    @ahoopes
    ahoopes committed Sep 19, 2020
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Commits on Oct 3, 2020

  1. cleaup README a bit

    @ahoopes
    ahoopes committed Oct 3, 2020
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Commits on Oct 4, 2020

  1. adding tutorial

    @adalca
    adalca committed Oct 4, 2020
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  2. grouping notes

    @adalca
    adalca committed Oct 4, 2020
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  3. Update README.md

    @adalca
    adalca committed Oct 4, 2020
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Commits on Oct 5, 2020

  1. updated TemplateCreation so it doesn't require an atlas input

    @brf2
    brf2 committed Oct 5, 2020
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Commits on Oct 6, 2020

  1. Revert "updated TemplateCreation so it doesn't require an atlas input"

    @ahoopes
    ahoopes committed Oct 6, 2020
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Commits on Oct 7, 2020

  1. add install instructions to README

    @ahoopes
    ahoopes committed Oct 7, 2020
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  2. Merge pull request #221 from voxelmorph/dev 

    Add install instructions to README
    @voxelmorph
    voxelmorph committed Oct 7, 2020
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Commits on Nov 30, 2020

  1. removing GPL

    @voxelmorph
    voxelmorph committed Nov 30, 2020
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  2. Create LICENSE 

    switching to Apache 2.0
    @voxelmorph
    voxelmorph committed Nov 30, 2020
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Commits on Dec 9, 2020

  1. Update README.md

    @voxelmorph
    voxelmorph committed Dec 9, 2020
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Commits on Apr 8, 2021

  1. Update Apache license in setup.py (#295)

    @yanlend
    yanlend committed Apr 8, 2021
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