voxelmorph 0.1__tar.gz → 0.3__tar.gz

voxelmorph-0.3/LICENSE.md

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

voxelmorph-0.3/PKG-INFO

@@ -0,0 +1,245 @@
+Metadata-Version: 2.4
+Name: voxelmorph
+Version: 0.3
+Summary: Image Registration with Convolutional Networks
+Home-page: https://github.com/voxelmorph/voxelmorph
+Author: Adrian V. Dalca, Malte Hoffmann, Andrew Hoopes
+License-Expression: Apache-2.0
+Project-URL: GitHub, https://github.com/voxelmorph/voxelmorph
+Project-URL: PyPI, https://pypi.org/project/voxelmorph/
+Keywords: python,pytorch,medical-imaging,registration,medical-image-computing
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: torch
+Requires-Dist: scikit-image
+Requires-Dist: packaging
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: nibabel
+Requires-Dist: h5py
+Requires-Dist: neurite>=0.2
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-python
+
+# VoxelMorph: learning-based image registration
+
+**VoxelMorph** is a general purpose library for learning-based tools for alignment/registration, and more generally modelling with deformations.
+
+> ⚠️ **Warning**: VoxelMorph pytorch is under active development. Interfaces may change.
+
+> **For users who want to use the stable TensorFlow version**, pull or clone the [`dev-tensorflow`](https://github.com/voxelmorph/voxelmorph/tree/dev-tensorflow) branch.
+
+## Install
+
+Install the published package from PyPI:
+
+```
+pip install voxelmorph
+```
+
+To work from a source checkout, clone this repository and install the requirements listed in `setup.py`.
+
+### Pre-commit hooks
+
+This repo uses `pre-commit` to run `pycodestyle` before commits.
+
+Install once after cloning:
+
+```bash
+pip install pre-commit
+pre-commit install
+```
+
+You can also run the check manually:
+
+```bash
+pre-commit run pycodestyle --all-files
+```
+
+# Tutorial
+
+We have several VoxelMorph tutorials:
+  - the main [VoxelMorph tutorial](http://tutorial.voxelmorph.net/) explains VoxelMorph and learning-based registration
+  - a [deformable SynthMorph demo](https://colab.research.google.com/drive/1zaDnAJGUokS0knqWttuTgrRJMb6zxukI?usp=sharing) showing how to train a registration model without data
+  - an [affine SynthMorph demo](https://colab.research.google.com/drive/1QClknfaZIYklBjmBy-nUn83h85bpo8r0?usp=sharing) on learning anatomy-aware and acquisition-agnostic affine registration
+  - a [CT-to-MRI SynthMorph demo](https://colab.research.google.com/drive/1aWbFiyQw5mtJbTglpniAOMimGo_l8BYP?usp=drive_link) clipping the Hounsfield scale for multi-modal registration
+  - a [SynthMorph shapes demo](https://colab.research.google.com/drive/14s2h0j_Aoncp587vmpjsQBe6PQTxyVP5) that walks through the steps of running a trained 3D shapes model
+  - a [tutorial on training VoxelMorph](https://colab.research.google.com/drive/1ZefmWXBupRNsnIbBbGquhVDsk-7R7L1S?usp=sharing) on [OASIS data](https://github.com/adalca/medical-datasets/blob/master/neurite-oasis.md), which we processed and released for free for HyperMorph
+  - an [additional small tutorial](https://colab.research.google.com/drive/1V0CutSIfmtgDJg1XIkEnGteJuw0u7qT-#scrollTo=h1KXYz-Nauwn) on warping annotations together with images
+  - another tutorial on [template (atlas) construction](https://colab.research.google.com/drive/1SkQbrWTQHpQFrG4J2WoBgGZC9yAzUas2?usp=sharing) with VoxelMorph
+  - visualize [warp](https://colab.research.google.com/drive/1F8f1imh5WfyBv-crllfeJBFY16-KHl9c?usp=sharing) as warped grid
+  - [inverting warps](https://colab.research.google.com/drive/1juAJRYhPPDNbO9yRtlc0VGhbIFSuhpJ2?usp=sharing) that are not diffeomorphisms
+
+
+# Instructions
+
+To use the VoxelMorph library from source, clone this repository and install the requirements listed in `setup.py`.
+
+> **Note**: For source development, install from GitHub instead:
+
+```
+pip install git+https://github.com/voxelmorph/voxelmorph.git
+```
+
+## Pre-trained models
+
+See list of pre-trained models available [here](data/readme.md#models).
+
+## Training
+
+If you would like to train your own model, you will likely need to customize some of the data-loading code in `voxelmorph/generators.py` for your own datasets and data formats. However, it is possible to run many of the example scripts out-of-the-box, assuming that you provide a list of filenames in the training dataset. Training data can be in the NIfTI, MGZ, or npz (numpy) format, and it's assumed that each npz file in your data list has a `vol` parameter, which points to the image data to be registered, and an optional `seg` variable, which points to a corresponding discrete segmentation (for semi-supervised learning). It's also assumed that the shape of all training image data is consistent, but this, of course, can be handled in a customized generator if desired.
+
+For a given image list file `/images/list.txt` and output directory `/models/output`, the following script will train an image-to-image registration network (described in MICCAI 2018 by default) with an unsupervised loss. Model weights will be saved to a path specified by the `--model-dir` flag.
+
+```
+./scripts/tf/train.py --img-list /images/list.txt --model-dir /models/output --gpu 0
+```
+
+The `--img-prefix` and `--img-suffix` flags can be used to provide a consistent prefix or suffix to each path specified in the image list. Image-to-atlas registration can be enabled by providing an atlas file, e.g. `--atlas atlas.npz`. If you'd like to train using the original dense CVPR network (no diffeomorphism), use the `--int-steps 0` flag to specify no flow integration steps. Use the `--help` flag to inspect all of the command line options that can be used to fine-tune network architecture and training.
+
+
+## Registration
+
+If you simply want to register two images, you can use the `register.py` script with the desired model file. For example, if we have a model `model.h5` trained to register a subject (moving) to an atlas (fixed), we could run:
+
+```
+./scripts/tf/register.py --moving moving.nii.gz --fixed atlas.nii.gz --moved warped.nii.gz --model model.h5 --gpu 0
+```
+
+This will save the moved image to `warped.nii.gz`. To also save the predicted deformation field, use the `--save-warp` flag. Both npz or nifty files can be used as input/output in this script.
+
+
+## Testing (measuring Dice scores)
+
+To test the quality of a model by computing dice overlap between an atlas segmentation and warped test scan segmentations, run:
+
+```
+./scripts/tf/test.py --model model.h5 --atlas atlas.npz --scans scan01.npz scan02.npz scan03.npz --labels labels.npz
+```
+
+Just like for the training data, the atlas and test npz files include `vol` and `seg` parameters and the `labels.npz` file contains a list of corresponding anatomical labels to include in the computed dice score.
+
+
+## Parameter choices
+
+
+### CVPR version
+
+For the CC loss function, we found a reg parameter of 1 to work best. For the MSE loss function, we found 0.01 to work best.
+
+
+### MICCAI version
+
+For our data, we found `image_sigma=0.01` and `prior_lambda=25` to work best.
+
+In the original MICCAI code, the parameters were applied after the scaling of the velocity field. With the newest code, this has been "fixed", with different default parameters reflecting the change. We recommend running the updated code. However, if you'd like to run the very original MICCAI2018 mode, please use `xy` indexing and `use_miccai_int` network option, with MICCAI2018 parameters.
+
+
+## Spatial transforms and integration
+
+- The spatial transform code, found at `voxelmorph.layers.SpatialTransformer`, accepts N-dimensional affine and dense transforms, including linear and nearest neighbor interpolation options. Note that original development of VoxelMorph used `xy` indexing, whereas we are now emphasizing `ij` indexing.
+
+- For the MICCAI2018 version, we integrate the velocity field using `voxelmorph.layers.VecInt`. By default we integrate using scaling and squaring, which we found efficient.
+
+
+# VoxelMorph papers
+
+If you use VoxelMorph or some part of the code, please cite (see [bibtex](citations.bib)):
+
+  * HyperMorph, avoiding the need to tune registration hyperparameters:   
+
+    **Learning the Effect of Registration Hyperparameters with HyperMorph**  
+    Andrew Hoopes, [Malte Hoffmann](https://malte.cz), Bruce Fischl, [John Guttag](https://people.csail.mit.edu/guttag/), [Adrian V. Dalca](http://adalca.mit.edu)  
+    MELBA: Machine Learning for Biomedical Imaging. 2022. [eprint arXiv:2203.16680](https://arxiv.org/abs/2203.16680)
+
+    **HyperMorph: Amortized Hyperparameter Learning for Image Registration.**  
+    Andrew Hoopes, [Malte Hoffmann](https://malte.cz), Bruce Fischl, [John Guttag](https://people.csail.mit.edu/guttag/), [Adrian V. Dalca](http://adalca.mit.edu)  
+    IPMI: Information Processing in Medical Imaging. 2021. [eprint arXiv:2101.01035](https://arxiv.org/abs/2101.01035)
+
+  * [SynthMorph](https://synthmorph.voxelmorph.net), avoiding the need to have data at training (!):  
+
+    **Anatomy-aware and acquisition-agnostic joint registration with SynthMorph.**  
+    [Malte Hoffmann](https://malte.cz), Andrew Hoopes, Douglas N. Greve, Bruce Fischl, [Adrian V. Dalca](http://adalca.mit.edu)  
+    Imaging Neuroscience. 2024. [eprint arXiv:2301.11329](https://arxiv.org/abs/2301.11329)
+
+    **Anatomy-specific acquisition-agnostic affine registration learned from fictitious images.**  
+    [Malte Hoffmann](https://malte.cz), Andrew Hoopes, Bruce Fischl, [Adrian V. Dalca](http://adalca.mit.edu)  
+    SPIE Medical Imaging: Image Processing. 2023.
+
+    **SynthMorph: learning contrast-invariant registration without acquired images.**  
+    [Malte Hoffmann](https://malte.cz), Benjamin Billot, [Juan Eugenio Iglesias](https://scholar.harvard.edu/iglesias), Bruce Fischl, [Adrian V. Dalca](http://adalca.mit.edu)  
+    IEEE TMI: Transactions on Medical Imaging. 2022. [eprint arXiv:2004.10282](https://arxiv.org/abs/2004.10282)
+
+  * For the atlas formation model:  
+  
+    **Learning Conditional Deformable Templates with Convolutional Networks**  
+  [Adrian V. Dalca](http://adalca.mit.edu), [Marianne Rakic](https://mariannerakic.github.io/), [John Guttag](https://people.csail.mit.edu/guttag/), [Mert R. Sabuncu](http://sabuncu.engineering.cornell.edu/)  
+  NeurIPS 2019. [eprint arXiv:1908.02738](https://arxiv.org/abs/1908.02738)
+
+  * For the diffeomorphic or probabilistic model:
+
+    **Unsupervised Learning of Probabilistic Diffeomorphic Registration for Images and Surfaces**  
+[Adrian V. Dalca](http://adalca.mit.edu), [Guha Balakrishnan](http://people.csail.mit.edu/balakg/), [John Guttag](https://people.csail.mit.edu/guttag/), [Mert R. Sabuncu](http://sabuncu.engineering.cornell.edu/)  
+MedIA: Medial Image Analysis. 2019. [eprint arXiv:1903.03545](https://arxiv.org/abs/1903.03545) 
+
+    **Unsupervised Learning for Fast Probabilistic Diffeomorphic Registration**  
+[Adrian V. Dalca](http://adalca.mit.edu), [Guha Balakrishnan](http://people.csail.mit.edu/balakg/), [John Guttag](https://people.csail.mit.edu/guttag/), [Mert R. Sabuncu](http://sabuncu.engineering.cornell.edu/)  
+MICCAI 2018. [eprint arXiv:1805.04605](https://arxiv.org/abs/1805.04605)
+
+  * For the original CNN model, MSE, CC, or segmentation-based losses:
+
+    **VoxelMorph: A Learning Framework for Deformable Medical Image Registration**  
+[Guha Balakrishnan](http://people.csail.mit.edu/balakg/), [Amy Zhao](http://people.csail.mit.edu/xamyzhao/), [Mert R. Sabuncu](http://sabuncu.engineering.cornell.edu/), [John Guttag](https://people.csail.mit.edu/guttag/), [Adrian V. Dalca](http://adalca.mit.edu)  
+IEEE TMI: Transactions on Medical Imaging. 2019. 
+[eprint arXiv:1809.05231](https://arxiv.org/abs/1809.05231)
+
+    **An Unsupervised Learning Model for Deformable Medical Image Registration**  
+[Guha Balakrishnan](http://people.csail.mit.edu/balakg/), [Amy Zhao](http://people.csail.mit.edu/xamyzhao/), [Mert R. Sabuncu](http://sabuncu.engineering.cornell.edu/), [John Guttag](https://people.csail.mit.edu/guttag/), [Adrian V. Dalca](http://adalca.mit.edu)  
+CVPR 2018. [eprint arXiv:1802.02604](https://arxiv.org/abs/1802.02604)
+
+
+# Notes
+- **keywords**: machine learning, convolutional neural networks, alignment, mapping, registration  
+- **data in papers**: 
+In our initial papers, we used publicly available data, but unfortunately we cannot redistribute it (due to the constraints of those datasets). We do a certain amount of pre-processing for the brain images we work with, to eliminate sources of variation and be able to compare algorithms on a level playing field. In particular, we perform FreeSurfer `recon-all` steps up to skull stripping and affine normalization to Talairach space, and crop the images via `((48, 48), (31, 33), (3, 29))`. 
+
+We encourage users to download and process their own data. See [a list of medical imaging datasets here](https://github.com/adalca/medical-datasets). Note that you likely do not need to perform all of the preprocessing steps, and indeed VoxelMorph has been used in other work with other data.
+
+
+# Creation of deformable templates
+
+To experiment with this method, please use `train_template.py` for unconditional templates and `train_cond_template.py` for conditional templates, which use the same conventions as VoxelMorph (please note that these files are less polished than the rest of the VoxelMorph library).
+
+We've also provided an unconditional atlas in `data/generated_uncond_atlas.npz.npy`. 
+
+Models in h5 format weights are provided for [unconditional atlas here](http://people.csail.mit.edu/adalca/voxelmorph/atlas_creation_uncond_NCC_1500.h5), and [conditional atlas here](http://people.csail.mit.edu/adalca/voxelmorph/atlas_creation_cond_NCC_1022.h5).
+
+**Explore the atlases [interactively here](http://voxelmorph.mit.edu/atlas_creation/)** with tipiX!
+
+
+# SynthMorph
+
+SynthMorph is a strategy for learning registration without acquired imaging data, producing powerful networks agnostic to contrast induced by MRI ([eprint arXiv:2004.10282](https://arxiv.org/abs/2004.10282)). For a video and a demo showcasing the steps of generating random label maps from noise distributions and using these to train a network, visit [synthmorph.voxelmorph.net](https://synthmorph.voxelmorph.net).
+
+We provide model files for a ["shapes" variant](https://surfer.nmr.mgh.harvard.edu/ftp/data/voxelmorph/synthmorph/shapes-dice-vel-3-res-8-16-32-256f.h5) of SynthMorph, that we train using images synthesized from random shapes only, and a ["brains" variant](https://surfer.nmr.mgh.harvard.edu/ftp/data/voxelmorph/synthmorph/brains-dice-vel-0.5-res-16-256f.h5), that we train using images synthesized from brain label maps. We train the brains variant by optimizing a loss term that measures volume overlap of a [selection of brain labels](https://surfer.nmr.mgh.harvard.edu/ftp/data/voxelmorph/synthmorph/fs-labels.npy). For registration with either model, please use the `register.py` script with the respective model weights.
+
+Accurate registration requires the input images to be min-max normalized, such that voxel intensities range from 0 to 1, and to be resampled in the affine space of a [reference image](https://surfer.nmr.mgh.harvard.edu/ftp/data/voxelmorph/synthmorph/ref.nii.gz). The affine registration can be performed with a variety of packages, and we choose FreeSurfer. First, we skull-strip the images with [SAMSEG](https://surfer.nmr.mgh.harvard.edu/fswiki/Samseg), keeping brain labels only. Second, we run [mri_robust_register](https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_register):
+
+```
+mri_robust_register --mov in.nii.gz --dst out.nii.gz --lta transform.lta --satit --iscale
+mri_robust_register --mov in.nii.gz --dst out.nii.gz --lta transform.lta --satit --iscale --ixform transform.lta --affine
+```
+
+where we replace `--satit --iscale` with `--cost NMI` for registration across MRI contrasts.
+
+
+# Data
+While we cannot release most of the data used in the VoxelMorph papers as they prohibit redistribution, we thorough processed and [re-released OASIS1](https://github.com/adalca/medical-datasets/blob/master/neurite-oasis.md) while developing [HyperMorph](http://hypermorph.voxelmorph.net/). We now include a quick [VoxelMorph tutorial](https://colab.research.google.com/drive/1ZefmWXBupRNsnIbBbGquhVDsk-7R7L1S?usp=sharing) to train VoxelMorph on neurite-oasis data.
+
+# Contact
+For any code-related problems or questions please [open an issue](https://github.com/voxelmorph/voxelmorph/issues/new?labels=voxelmorph) or [start a discussion](https://github.com/voxelmorph/voxelmorph/discussions) of general registration/VoxelMorph topics.