Description

Detailed whole brain segmentation is an essential quantitative technique in medical image analysis, which provides a non-invasive way of measuring brain regions from a clinical acquired structural magnetic resonance imaging (MRI). We provide the pre-trained model for training and inferencing whole brain segmentation with 133 structures. Training pipeline is provided to support active learning in MONAI Label and training with bundle.

A tutorial and release of model for whole brain segmentation using the 3D transformer-based segmentation model UNEST.

Authors: Xin Yu ([email protected])

Yinchi Zhou ([email protected]) | Yucheng Tang ([email protected])

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Fig.1 - The demonstration of T1w MRI images registered in MNI space and the whole brain segmentation labels with 133 classes

Model Overview

A pre-trained UNEST base model [1] for volumetric (3D) whole brain segmentation with T1w MR images. To leverage information across embedded sequences, ”shifted window” transformers are proposed for dense predictions and modeling multi-scale features. However, these attempts that aim to complicate the self-attention range often yield high computation complexity and data inefficiency. Inspired by the aggregation function in the nested ViT, we propose a new design of a 3D U-shape medical segmentation model with Nested Transformers (UNesT) hierarchically with the 3D block aggregation function, that learn locality behaviors for small structures or small dataset. This design retains the original global self-attention mechanism and achieves information communication across patches by stacking transformer encoders hierarchically.

Fig.2 - The network architecture of UNEST Base model

Data

The training data is from the Vanderbilt University and Vanderbilt University Medical Center with public released OASIS and CANDI datsets. Training and testing data are MRI T1-weighted (T1w) 3D volumes coming from 3 different sites. There are a total of 133 classes in the whole brain segmentation task. Among 50 T1w MRI scans from Open Access Series on Imaging Studies (OASIS) (Marcus et al., 2007) dataset, 45 scans are used for training and the other 5 for validation. The testing cohort contains Colin27 T1w scan (Aubert-Broche et al., 2006) and 13 T1w MRI scans from the Child and Adolescent Neuro Development Initiative (CANDI) (Kennedy et al., 2012). All data are registered to the MNI space using the MNI305 (Evans et al., 1993) template and preprocessed follow the method in (Huo et al., 2019). Input images are randomly cropped to the size of 96 × 96 × 96.

Important

The brain MRI images for training are registered to Affine registration from the target image to the MNI305 template using NiftyReg. The data should be in the MNI305 space before inference.

If your images are already in MNI space, skip the registration step.

You could use any resitration tool to register image to MNI space. Here is an example using ants. Registration to MNI Space: Sample suggestion. E.g., use ANTS or other tools for registering T1 MRI image to MNI305 Space.

pip install antspyx

#Sample ANTS registration

import ants
import sys
import os

fixed_image = ants.image_read('<fixed_image_path>')
moving_image = ants.image_read('<moving_image_path>')
transform = ants.registration(fixed_image,moving_image,'Affine')

reg3t = ants.apply_transforms(fixed_image,moving_image,transform['fwdtransforms'][0])
ants.image_write(reg3t,output_image_path)

Training configuration

The training and inference was performed with at least one 24GB-memory GPU.

Actual Model Input: 96 x 96 x 96

Input and output formats

Input: 1 channel T1w MRI image in MNI305 Space.

commands example

Download trained checkpoint model to ./model/model.pt:

Add scripts component: To run the workflow with customized components, PYTHONPATH should be revised to include the path to the customized component:

export PYTHONPATH=$PYTHONPATH: '<path to the bundle root dir>/'

Execute Training:

python -m monai.bundle run training --meta_file configs/metadata.json --config_file configs/train.json --logging_file configs/logging.conf

Execute inference:

python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file configs/inference.json --logging_file configs/logging.conf

More examples output

Fig.3 - The output prediction comparison with variant and ground truth

Training/Validation Benchmarking

A graph showing the training accuracy for fine-tuning 600 epochs.

With 10 fine-tuned labels, the training process converges fast.

Complete ROI of the whole brain segmentation

133 brain structures are segmented.

#1	#2	#3	#4
0: background	1 : 3rd-Ventricle	2 : 4th-Ventricle	3 : Right-Accumbens-Area
4 : Left-Accumbens-Area	5 : Right-Amygdala	6 : Left-Amygdala	7 : Brain-Stem
8 : Right-Caudate	9 : Left-Caudate	10 : Right-Cerebellum-Exterior	11 : Left-Cerebellum-Exterior
12 : Right-Cerebellum-White-Matter	13 : Left-Cerebellum-White-Matter	14 : Right-Cerebral-White-Matter	15 : Left-Cerebral-White-Matter
16 : Right-Hippocampus	17 : Left-Hippocampus	18 : Right-Inf-Lat-Vent	19 : Left-Inf-Lat-Vent
20 : Right-Lateral-Ventricle	21 : Left-Lateral-Ventricle	22 : Right-Pallidum	23 : Left-Pallidum
24 : Right-Putamen	25 : Left-Putamen	26 : Right-Thalamus-Proper	27 : Left-Thalamus-Proper
28 : Right-Ventral-DC	29 : Left-Ventral-DC	30 : Cerebellar-Vermal-Lobules-I-V	31 : Cerebellar-Vermal-Lobules-VI-VII
32 : Cerebellar-Vermal-Lobules-VIII-X	33 : Left-Basal-Forebrain	34 : Right-Basal-Forebrain	35 : Right-ACgG--anterior-cingulate-gyrus
36 : Left-ACgG--anterior-cingulate-gyrus	37 : Right-AIns--anterior-insula	38 : Left-AIns--anterior-insula	39 : Right-AOrG--anterior-orbital-gyrus
40 : Left-AOrG--anterior-orbital-gyrus	41 : Right-AnG---angular-gyrus	42 : Left-AnG---angular-gyrus	43 : Right-Calc--calcarine-cortex
44 : Left-Calc--calcarine-cortex	45 : Right-CO----central-operculum	46 : Left-CO----central-operculum	47 : Right-Cun---cuneus
48 : Left-Cun---cuneus	49 : Right-Ent---entorhinal-area	50 : Left-Ent---entorhinal-area	51 : Right-FO----frontal-operculum
52 : Left-FO----frontal-operculum	53 : Right-FRP---frontal-pole	54 : Left-FRP---frontal-pole	55 : Right-FuG---fusiform-gyrus
56 : Left-FuG---fusiform-gyrus	57 : Right-GRe---gyrus-rectus	58 : Left-GRe---gyrus-rectus	59 : Right-IOG---inferior-occipital-gyrus ,
60 : Left-IOG---inferior-occipital-gyrus	61 : Right-ITG---inferior-temporal-gyrus	62 : Left-ITG---inferior-temporal-gyrus	63 : Right-LiG---lingual-gyrus
64 : Left-LiG---lingual-gyrus	65 : Right-LOrG--lateral-orbital-gyrus	66 : Left-LOrG--lateral-orbital-gyrus	67 : Right-MCgG--middle-cingulate-gyrus
68 : Left-MCgG--middle-cingulate-gyrus	69 : Right-MFC---medial-frontal-cortex	70 : Left-MFC---medial-frontal-cortex	71 : Right-MFG---middle-frontal-gyrus
72 : Left-MFG---middle-frontal-gyrus	73 : Right-MOG---middle-occipital-gyrus	74 : Left-MOG---middle-occipital-gyrus	75 : Right-MOrG--medial-orbital-gyrus
76 : Left-MOrG--medial-orbital-gyrus	77 : Right-MPoG--postcentral-gyrus	78 : Left-MPoG--postcentral-gyrus	79 : Right-MPrG--precentral-gyrus
80 : Left-MPrG--precentral-gyrus	81 : Right-MSFG--superior-frontal-gyrus	82 : Left-MSFG--superior-frontal-gyrus	83 : Right-MTG---middle-temporal-gyrus
84 : Left-MTG---middle-temporal-gyrus	85 : Right-OCP---occipital-pole	86 : Left-OCP---occipital-pole	87 : Right-OFuG--occipital-fusiform-gyrus
88 : Left-OFuG--occipital-fusiform-gyrus	89 : Right-OpIFG-opercular-part-of-the-IFG	90 : Left-OpIFG-opercular-part-of-the-IFG	91 : Right-OrIFG-orbital-part-of-the-IFG
92 : Left-OrIFG-orbital-part-of-the-IFG	93 : Right-PCgG--posterior-cingulate-gyrus	94 : Left-PCgG--posterior-cingulate-gyrus	95 : Right-PCu---precuneus
96 : Left-PCu---precuneus	97 : Right-PHG---parahippocampal-gyrus	98 : Left-PHG---parahippocampal-gyrus	99 : Right-PIns--posterior-insula
100 : Left-PIns--posterior-insula	101 : Right-PO----parietal-operculum	102 : Left-PO----parietal-operculum	103 : Right-PoG---postcentral-gyrus
104 : Left-PoG---postcentral-gyrus	105 : Right-POrG--posterior-orbital-gyrus	106 : Left-POrG--posterior-orbital-gyrus	107 : Right-PP----planum-polare
108 : Left-PP----planum-polare	109 : Right-PrG---precentral-gyrus	110 : Left-PrG---precentral-gyrus	111 : Right-PT----planum-temporale
112 : Left-PT----planum-temporale	113 : Right-SCA---subcallosal-area	114 : Left-SCA---subcallosal-area	115 : Right-SFG---superior-frontal-gyrus
116 : Left-SFG---superior-frontal-gyrus	117 : Right-SMC---supplementary-motor-cortex	118 : Left-SMC---supplementary-motor-cortex	119 : Right-SMG---supramarginal-gyrus
120 : Left-SMG---supramarginal-gyrus	121 : Right-SOG---superior-occipital-gyrus	122 : Left-SOG---superior-occipital-gyrus	123 : Right-SPL---superior-parietal-lobule
124 : Left-SPL---superior-parietal-lobule	125 : Right-STG---superior-temporal-gyrus	126 : Left-STG---superior-temporal-gyrus	127 : Right-TMP---temporal-pole
128 : Left-TMP---temporal-pole	129 : Right-TrIFG-triangular-part-of-the-IFG	130 : Left-TrIFG-triangular-part-of-the-IFG	131 : Right-TTG---transverse-temporal-gyrus
132 : Left-TTG---transverse-temporal-gyrus

Bundle Integration in MONAI Lable

The inference and training pipleine can be easily used by the MONAI Label server and 3D Slicer for fast labeling T1w MRI images in MNI space.

Disclaimer

This is an example, not to be used for diagnostic purposes.

References

[1] Yu, Xin, Yinchi Zhou, Yucheng Tang et al. Characterizing Renal Structures with 3D Block Aggregate Transformers. arXiv preprint arXiv:2203.02430 (2022). https://arxiv.org/pdf/2203.02430.pdf

[2] Zizhao Zhang et al. Nested Hierarchical Transformer: Towards Accurate, Data-Efficient and Interpretable Visual Understanding. AAAI Conference on Artificial Intelligence (AAAI) 2022

[3] Huo, Yuankai, et al. 3D whole brain segmentation using spatially localized atlas network tiles. NeuroImage 194 (2019): 105-119.

License

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.