Webapps
Neurodesk offers a set of browser-native webapps for protocol comparison, QSM processing, medical image segmentation and many more tasks. They run directly in the browser, so there is no desktop installation step before you can start working. Browse the complete list in the Neurodesk Webapps directory.
ANTs aligns MRI images using affine and SyN deformable registration.
Brain extraction
Section titled “Brain extraction”webapps.neurodesk.org/brain-extraction
Extract brain tissue and masks using BET, MindGrab, or SynthStrip. This app is experimental.
Brain2Print
Section titled “Brain2Print”webapps.neurodesk.org/brain2print
Brain2Print creates printable brain meshes from NIfTI or DICOM scans.
BrainChop
Section titled “BrainChop”BrainChop segments brain images in the browser. Load a NIfTI image to view and save its segmentation.
BrowserQC
Section titled “BrowserQC”webapps.neurodesk.org/browserqc
BrowserQC segments MRI scans and calculates image quality metrics.
CALMaR: Co-designed Automated Lesion Mapping and Reporting
Section titled “CALMaR: Co-designed Automated Lesion Mapping and Reporting”CALMaR performs brain extraction, lesion masking, MNI registration, atlas overlap, functional-connectivity mapping, and reportable tables for stroke lesions.
Deface
Section titled “Deface”Deface removes identifying facial features from MRI scans.
dicompare
Section titled “dicompare”webapps.neurodesk.org/dicompare
dicompare is a browser-based tool for sharing, comparing, and validating DICOM acquisition protocols. It is useful when teams want to standardise scanner protocols across sites, compare local scans against agreed standards, and generate shareable schemas and compliance reports.
dwi2trx
Section titled “dwi2trx”dwi2trx fits diffusion tensors and reconstructs streamlines using the GPU.
Easy MP2RAGE T1 Map
Section titled “Easy MP2RAGE T1 Map”webapps.neurodesk.org/easy-mp2rage
Process MP2RAGE scans with T1 mapping, B1 correction, and UNI denoising.
EdgeReg
Section titled “EdgeReg”EdgeReg aligns MRI images using affine registration with niimath.
FireANTs
Section titled “FireANTs”webapps.neurodesk.org/fireants
FireANTs registers brain images using the CPU or WebGPU.
Greedy
Section titled “Greedy”Greedy aligns MRI images using affine and deformable registration.
MRI2VID
Section titled “MRI2VID”webapps.neurodesk.org/dicom2vid
MRI2VID converts DICOM, NIfTI, or MGZ volumes into scrolling videos.
MuscleMap
Section titled “MuscleMap”webapps.neurodesk.org/musclemap
MuscleMap performs browser-based muscle segmentation from MRI data. It is designed for whole-body and regional muscle analysis and provides an interactive viewer for reviewing segmentation outputs.
NiiMath
Section titled “NiiMath”NiiMath applies mathematical operations to images and displays the results.
QSMbly
Section titled “QSMbly”QSMbly provides a full Quantitative Susceptibility Mapping workflow in the browser. It supports DICOM and NIfTI input data and exposes the main preparation, masking, SWI, and QSM pipeline steps through a guided interface.
SeedSeg
Section titled “SeedSeg”SeedSeg performs browser-based segmentation of intraprostatic gold fiducial markers in prostate MRI using a 3D U-Net model. It supports DICOM and NIfTI input data.
Spinal Cord Toolbox
Section titled “Spinal Cord Toolbox”This is a browser-based implementation of the Spinal Cord Toolbox MRI segmentation workflows.
SurfAnnotate
Section titled “SurfAnnotate”webapps.neurodesk.org/surfannotate
SurfAnnotate displays cortical surfaces for manual region annotation and vertex selection.
SYNcro
Section titled “SYNcro”SYNcro normalizes brain scans and aligned lesion maps to MNI space.
SynthSeg
Section titled “SynthSeg”webapps.neurodesk.org/synthseg
SynthSeg segments brain MRI into regions labelled using FreeSurfer conventions.
SynthSR
Section titled “SynthSR”SynthSR synthesizes a 1 mm T1-weighted brain image.
TopoFit
Section titled “TopoFit”TopoFit reconstructs cortical white, pial, and registration surfaces from brain MRI.
VesselBoost
Section titled “VesselBoost”webapps.neurodesk.org/vesselboost
VesselBoost is a browser-based blood vessel segmentation tool. It combines preprocessing and inference steps in a guided workflow so users can segment vessel structures from MRI angiography data directly on their own machine.
ZARRo streams and displays multiscale OME-Zarr volumes.
Webapps from Neurodesk friends and family
Section titled “Webapps from Neurodesk friends and family”These browser-based webapps are built and maintained by collaborators in the wider Neurodesk community and are not maintained by us.
qMRust
Section titled “qMRust”qMRust provides methods from qMRLab for quantitative MRI processing in the browser.