关于最近一些MRI-T1w结构像处理pipeline的测试
FastSurfer -> 全脑分割
https://deep-mi.org/research/fastsurfer/ FastSurfer is a fast and extensively validated deep-learning pipeline for the fully automated processing of structural human brain MRIs. As such, it provides FreeSurfer conform outputs, enables scalable big-data analysis and time-critical clinical applications such as structure localization during image acquisition or extraction of quantitative measures.
# 完整分割(GPU)
docker run --gpus all -v /data/mg_data/mnt/bl_test/input:/data -v /data/mg_data/mnt/bl_test/fastsf_output:/output -v /data/freesurfer:/fs_license --rm deepmi/fastsurfer:gpu-v1.1.1 --fs_license /fs_license/freesurfer_license.txt --t1 /data/t1.nii --sid subject2 --sd /output --parallel
# DKT Lookup table
31和63作为脉络丛会被分割出来,应该当做LV,对应4和43
77作为WMH,没有区分左右,不便合并
SynthSeg -> 全脑分割,计算ICV
https://github.com/BBillot/SynthSeg https://surfer.nmr.mgh.harvard.edu/fswiki/SynthSeg
SynthSeg
可不依赖GPU,实测CPU多线程计算约2分钟内完成
# 分割 (完整)
mri_synthseg --i /dataio/t1.nii --parc --robust --vol /dataio/vol.csv --qc /dataio/qc.csv --threads 172 --o /dataio/t1_seg.nii.gz
# 注意 --resample如果输入本身是1mm iso,则不会生成resample图像
SynthStrip -> 剥头皮
https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/ SynthStrip is a skull-stripping tool that extracts brain signal from a landscape of image types, ranging across imaging modality, contrast, resolution, and subject population. It leverages a deep learning strategy that synthesizes arbitrary training images from segmentation maps to optimize a robust model agnostic to acquisition specifics. https://doi.org/10.1016/j.neuroimage.2022.119474
# 自动去头皮(多模态泛化性优秀),1分钟以内
mri_synthstrip -i /dataio/t1.nii -o /dataio/t1_bet.nii -m /dataio/t1_mask.nii
sbTIV-> 计算ICV
https://freesurfer.net/fswiki/Samseg https://freesurfer.net/fswiki/sbTIV Total intracranial volume (TIV/ICV) is an important covariate for volumetric analyses of the brain and brain regions. It is commonly used to correct for head size variation (i.e., ’normalize’ hippocampal volume size). The gold-standard method is manual delineation of T2 scans. Freesurfer currently provides the eTIV measure, described here. It has been shown to be a robust covariate.
## 计算sbTIV (segmentation-based TIV),大约5-10分钟
run_samseg --input /home/username/data/t1.nii --output /home/username/data/samsegOutput/ --threads 8
关于FreeSurfer图谱
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DK图谱lookuptable https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT https://www.cis.jhu.edu/~parky/MRN/Desikan%20Region%20Labels%20and%20Descriptions.pdf
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DKT 图谱: https://mindboggle.readthedocs.io/en/latest/labels.html
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HCPMMP图谱 : https://neuroimaging-core-docs.readthedocs.io/en/latest/pages/atlases.html