Documentation/Nightly/SlicerApplication/SupportedDataFormat
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File formats supported by Slicer Nightly
| Format | File Name Extensions | Read | Write | Module | |
|---|---|---|---|---|---|
| Scenes | Data | ||||
| MRML (Medical Reality Markup Language File) | .mrml | yes | yes | MRML file is a xml-formatted text file with scene metadata and pointers to externally stored data files. Data Model | |
| MRB (Medical Reality Bundle) | .mrb, .zip | yes | yes (.mrb extension only) | MRB is a binary format encapsulating all scene data (bulk data and metadata). Internally it uses zip format. Any .zip file that contains a self-contained data tree including a .mrml file can be opened. Coordinate system: RAS | |
| Slicer 2 Scene | .xml | yes | no | xml-formatted text file with scene metadata and pointers to externally stored data files. | Coordinate system: RAS |
| Data collections in XNAT Catalog format (".xcat") or XNAT Archive format (".xar") | .xcat | yes | no | ||
| Data collections in XNAT Archive format (".xar") | .xar | yes | no | ||
| Raster Images this includes 2D and 3D images, and more complicated types such as DWI or DTI |
Volumes | ||||
| DICOM | .dcm ... | yes[1] | no[2] | DICOM, DICOMToNRRDConverter, CreateDICOMSeries, Reporting extension. Coordinate system: LPS (specified by the DICOM standard) | |
| NRRD | .nrrd, .nhdr | yes | yes | Coordinate system: as defined in the file header (usually LPS) | |
| MetaImage | .mhd, .mha | yes | yes | Coordinate system: LPS (orientation information in the file header is ignored) | |
| VTK | .vtk | yes | yes | Coordinate system: LPS | |
| Analyze | .hdr, .img, .img.gz | yes | yes | ||
| NifTI | .nia, .nii, .nii.gz | yes | yes | ||
| BMP | .bmp | yes | yes | ||
| BioRad | .pic | yes | yes | ||
| Brains2 | .mask | yes | yes | ||
| GIPL | .gipl .gipl.gz | yes | yes | ||
| JPEG | .jpg, .jpeg | yes | yes | ||
| LSM | .lsm | yes | yes | ||
| PNG | .png | yes | yes | ||
| Stimulate | .spr | yes | yes | ||
| TIFF | .tif, .tiff | yes | yes | ||
| MGH-NMR | .mgz | yes | yes | ||
| MRC Electron Density | .mrc, .rec | yes | yes | ||
| Models | Models | ||||
| VTK Polygonal Data | .vtk | yes | yes | Coordinate system: RAS | |
| VTK XML Polygonal Data | .vtp | yes | yes | Coordinate system: RAS | |
| STL | .stl | yes | yes | coordinate system: RAS | |
| OBJ | .obj | yes | no | ||
| Freesurfer | .orig, .inflated, .sphere, .white, .smoothwm, .pial | yes | no | ||
| Others (to be tested) | .g, .byu | yes | no | ||
| Fiducials | Markups | ||||
| CSV | .fcsv | yes | yes | Coordinate system: RAS | |
| Text | .txt | yes | yes | Coordinate system: RAS | |
| Rulers | Annotations | ||||
| CSV | .acsv | yes | yes | Coordinate system: RAS | |
| Text | .txt | yes | yes | Coordinate system: RAS | |
| Transforms | Transforms | ||||
| ITK Transform | .tfm, .txt | yes | yes | linear and b-spline transform; Coordinate system: LPS | |
| Matlab MAT-File | .mat | yes | yes | linear and b-spline transform; Coordinate system: LPS | |
| Displacement field | .nrrd, .nhdr, .mha, .mhd, .nii, .nii.gz | yes | yes | grid transform; Coordinate system: LPS | |
| Transfer Functions | Volume Rendering | ||||
| Volume Rendering properties | .vp | yes | yes | ||
| Text | .txt | yes | yes | ||
| Lookup tables | Colors | ||||
| Text | .txt, .ctbl | yes | yes | ||
| Double Arrays | |||||
| CSV | .mcsv | yes | yes | ||
| Text | .txt | yes | yes | ||
- ↑ For a number of dMRI formats we recommend use of the DICOM to NRRD converter before loading the data into Slicer.
- ↑ Limited support for writing image volumes in DICOM format is provided by the Create DICOM Series module. Support of writing DICOM Segmentation Objects is provided by the Reporting extension
