Finding it hard to navigate the blooming field of fetal (and neonatal) brain MRI research, I summarize here some very useful tools for performing data processing and analysis.
| Software/Tool name |
![]() Tasks ![]() |
Data type |
Link |
![]() Visualization and edition 👀 ![]() |
| ITK Snap |
MRI visualization and segmentation |
Multiple formats, e.g. nifti, DICOM... |
|
| Kitware Glance |
Web application for object visualization |
Multiple formats, e.g. .vtk, .vtp... |
|
| MRICron |
MRI visualization & DICOM to Nifti conversion |
Multiple formats, e.g. nifti, DICOM... |
|
| Freeview |
(Included in Freesurfer) MRI and surface visualisation |
Multiple formats |
|
| Paraview |
Objects visualization and edition (images, meshes, glyphs...) |
Multiple formats, e.g. .vtk, .vtp... |
|
| Slicer 3D |
Images visualization, edition and segmentation |
.nii |
|
| MeshLab |
A comprehensive tool for editing meshes |
.ply, .stl |
|
![]() Quality ⭐ ![]() |
| fetal-brain-assessment |
Fetal MRI Quality Assessment |
Fetal MRI |
|
| FetMRQC |
Fetal MRI quality assessment and control |
Fetal MRI |
|
![]() Volume reconstruction 🧊 ![]() |
| NiftyMIC |
Brain extraction, super-resolution brain volume reconstruction, reorientation in standard radiological anatomical planes |
Fetal MRI |
|
| MIAL SRTK |
Brain extraction, super-resolution brain volume reconstruction, reorientation in standard radiological anatomical planes |
Fetal MRI |
|
| SVRTK |
Super-resolution volume reconstruction (including brain, body, heart, and placenta) |
Fetal MRI |
|
| BTK |
Super-resolution brain volume reconstruction, brain reorientation |
Fetal MRI |
|
| PVR |
Super-resolution brain volume reconstruction |
Fetal MRI |
|
| NeSVor |
Super-resolution brain volume reconstruction |
Fetal MRI |
|
![]() Brain segmentation ✂️ ![]() |
| MONAIfbs |
Fetal brain extraction |
Fetal MRI |
|
| Fetal brain seg |
Fetal brain extraction |
Fetal MRI |
|
| Trustworthy AI |
Fetal brain segmentation |
Fetal MRI |
|
| CasReg |
Fetal brain segmentation |
Fetal MRI |
|
| Uncertainty-Guided Interactive Refinement for Segmentation |
Fetal brain segmentation |
Fetal MRI |
|
| FetalCPseg |
Cortical plate segmentation |
Fetal MRI |
|
| Fetal MRI segmentation |
Cortical plate segmentation |
Fetal MRI |
|
| Brainbox |
Collaborative manual segmentation |
Any brain MRI |
|
![]() Cortical surface extraction 🧠 ![]() |
| dHCP structural pipeline |
Structural analysis including segmentation and cortical surface extraction |
Neonatal brain MRI (T1 & T2) |
|
| Perinatal pipeline |
Built on the dHCP pipeline. Super-resolution reconstruction, tissue segmentation |
Fetal and neonatal brain MRI (T1 & T2) |
|
| M-CRIBS pipeline |
Freesurfer-like pipeline for tissue segmentation and cortical surface extraction |
Neonatal brain MRI (T1 & T2) |
|
| Infant FreeSurfer |
Segmentation and surface extraction |
T1 infant MRI |
|
| MIRTK |
Segmentation and surface extraction |
T1 adult and neonatal MRI |
|
![]() Analysis ![]() |
| structural-pipeline-measures |
Volume and cortical surface measurements |
Neonatal brain MRI (T1 & T2) |
|