Documentation/4.8/SlicerApplication/SupportedDataFormat

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File formats supported by Slicer 4.8

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] 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[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
  1. For a number of dMRI formats we recommend use of the DICOM to NRRD converter before loading the data into Slicer.
  2. 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
  3. 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.

References