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. See Data Model. Coordinate system: RAS |
| 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] | yes (some data types)[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). Segmentation nodes are stored usually with .seg.nrrd extension, as 4D volumes (each 3D volume corresponds to a segment) with some additional custom fields. |
| MetaImage | .mhd, .mha | yes | yes | Coordinate system: LPS[3] (AnatomicalOrientation 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 |
| VTK Unstructured Grid Data | .vtk | yes | yes | Coordinate system: RAS |
| VTK XML Unstructured Grid Data | .vtp | yes | yes | Coordinate system: RAS |
| STL | .stl | yes | yes | Coordinate system: RAS |
| OBJ | .obj | yes | yes | Coordinate system: RAS |
| 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 | .h5 | yes | yes | For linear, b-spline, grid (displacement field), thin-plate spline, and composite transforms. Coordinate system: LPS |
| ITK Transform | .tfm, .txt | yes | yes | For linear, b-spline, and thin-plate spline, and composite transforms. Coordinate system: LPS |
| Matlab MAT-File | .mat | yes | yes | For linear and b-spline transforms. Coordinate system: LPS |
| Displacement field | .nrrd, .nhdr, .mha, .mhd, .nii, .nii.gz | yes | yes | For 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.
- ↑ Image volumes, RT structure sets, dose volumes, etc. can be exported using DICOM module's export feature. 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
- ↑ According to MetaIO naming scheme DICOM 'LPS' direction is 'RAI'.
What if your data is not supported?
If you have a file of binary data and you know the data is uncompressed and you know the way it is laid out in memory, then one way to load it in Slicer is to create a .nhdr file that points to the binary file.
A way to get started is to download sample data that is similar to your data (e.g. a CT or MR). Then save that data in .nhdr format and start editing the file to match your data.
Refer to the NRRD format documentation to see what the keys mean.
