Utilities¶
General-purpose neuroimaging utilities. Used for format conversion, image math, resampling, and quality control.
FSL¶
Docker image: brainlife/fsl
Image Math¶
| Tool | Description |
|---|---|
| FSL Mathematical Image Operations (fslmaths) | Performs a wide range of voxelwise mathematical operations on NIfTI images including arithmetic, filtering, threshold... |
| FSL Image Statistics (fslstats) | Computes various summary statistics from image data, optionally within a mask region. |
| FSL Region of Interest Extraction (fslroi) | Extracts a spatial or temporal sub-region from NIfTI images. |
| FSL Mean Time Series Extraction (fslmeants) | Extracts the mean time series from a 4D dataset within a mask or at specified coordinates. |
Volume Operations¶
| Tool | Description |
|---|---|
| FSL Volume Split (fslsplit) | Splits a 4D time series into individual 3D volumes or splits along any spatial axis. |
| FSL Volume Merge (fslmerge) | Concatenates multiple 3D volumes into a 4D time series or merges along any spatial axis. |
| FSL Reorient to Standard Orientation | Reorients images to match standard (MNI) orientation using 90-degree rotations and flips only. |
| FSL Robust Field of View Reduction | Automatically identifies and removes neck/non-brain tissue by estimating the brain center and reducing the field of v... |
| FSL Change File Type (fslchfiletype) | Converts neuroimaging files between NIfTI and ANALYZE file formats. |
Warp Utilities¶
| Tool | Description |
|---|---|
| FSL Apply Warp Field (applywarp) | Applies linear and/or non-linear warp fields to transform images between coordinate spaces. |
| FSL Invert Warp Field (invwarp) | Computes the inverse of a non-linear warp field for reverse transformations. |
| FSL Convert/Combine Warps (convertwarp) | Combines multiple warp fields and affine matrices into a single composite warp for efficient one-step transformation. |
Clustering¶
| Tool | Description |
|---|---|
| FSL Cluster Analysis (cluster) | Identifies contiguous clusters of suprathreshold voxels in statistical images and reports their properties. |
Image Info¶
| Tool | Description |
|---|---|
| FSL Header Display (fslhd) | Displays NIfTI/ANALYZE image header information including dimensions, voxel sizes, data type, and orientation. |
| FSL Image Info (fslinfo) | Displays concise image dimension and voxel size information from a NIfTI header. |
AFNI¶
Docker image: brainlife/afni
Image Math¶
| Tool | Description |
|---|---|
| AFNI 3D Voxelwise Calculator (3dcalc) | Voxelwise mathematical calculator supporting extensive expression syntax for operations on one or more datasets. |
| AFNI 3D Temporal Statistics (3dTstat) | Computes voxelwise temporal statistics (mean, stdev, median, etc.) across a 4D time series. |
Dataset Operations¶
| Tool | Description |
|---|---|
| AFNI 3D Dataset Information (3dinfo) | Displays header information and metadata from AFNI/NIfTI datasets. |
| AFNI 3D Dataset Copy (3dcopy) | Copies a dataset with optional format conversion between AFNI and NIfTI formats. |
| AFNI 3D Zero Padding (3dZeropad) | Adds zero-valued slices around dataset boundaries to extend the image matrix. |
| AFNI 3D Temporal Concatenate (3dTcat) | Concatenates datasets along the time dimension or selects specific sub-bricks from 4D data. |
ROI Utilities¶
| Tool | Description |
|---|---|
| AFNI 3D Undump (Coordinate to Volume) | Creates a 3D dataset from a text file containing voxel coordinates and values. |
| AFNI Atlas Location Query (whereami) | Reports anatomical atlas labels for given coordinates or identifies regions in multiple atlases simultaneously. |
| AFNI 3D Resample (3dresample) | Resamples a dataset to match the grid of another dataset or to a specified voxel size. |
| AFNI 3D Fractionize (ROI Resampling) | Resamples ROI/atlas datasets using fractional occupancy to maintain region representation at different resolutions. |
Warp Utilities¶
| Tool | Description |
|---|---|
| AFNI 3D Nonlinear Warp Apply | Applies precomputed nonlinear warps (from 3dQwarp) to transform datasets. |
| AFNI 3D Nonlinear Warp Concatenate | Concatenates multiple nonlinear warps and affine matrices into a single combined warp. |
ANTs¶
Docker image: antsx/ants
Preprocessing Utilities¶
| Tool | Description |
|---|---|
| ANTs N4 Bias Field Correction | Advanced bias field (intensity inhomogeneity) correction using the N4 algorithm with iterative B-spline fitting. |
| ANTs Non-Local Means Denoising | Reduces noise in MRI images using an adaptive non-local means algorithm that preserves structural details. |
Image Operations¶
| Tool | Description |
|---|---|
| ANTs Image Math Operations | Versatile tool for image arithmetic, morphological operations, distance transforms, and various measurements. |
| ANTs Image Thresholding | Applies various thresholding methods to create binary masks, including Otsu and k-means adaptive thresholding. |
Label Analysis¶
| Tool | Description |
|---|---|
| ANTs Label Geometry Measures | Computes geometric properties (volume, centroid, bounding box, eccentricity) for each labeled region in a parcellation. |
| ANTs Joint Label Fusion | Multi-atlas segmentation that combines labels from multiple pre-labeled atlases using joint label fusion with local w... |
Transform Utilities¶
| Tool | Description |
|---|---|
| ANTs Apply Transforms | Applies one or more precomputed transformations (affine + warp) to images, applying transforms in reverse order of sp... |
FreeSurfer¶
Docker image: freesurfer/freesurfer
Format Conversion¶
| Tool | Description |
|---|---|
| FreeSurfer MRI Format Conversion (mri_convert) | Converts between neuroimaging file formats (DICOM, NIfTI, MGH/MGZ, ANALYZE, etc.) with optional resampling and confor... |
dcm2niix¶
Docker image: xnat/dcm2niix
Format Conversion¶
| Tool | Description |
|---|---|
| DICOM to NIfTI Converter (dcm2niix) | Converts DICOM medical images to NIfTI format with BIDS-compatible JSON sidecar files, preserving acquisition metadata. |