Difference between revisions of "Documentation/Nightly/SlicerApplication/SupportedDataFormat"
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− | | xml-formatted text file with scene metadata and pointers to externally stored data files. | + | | xml-formatted text file with scene metadata and pointers to externally stored data files. Coordinate system: RAS |
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| Data collections in XNAT Catalog format (".xcat") or XNAT Archive format (".xar") | | Data collections in XNAT Catalog format (".xcat") or XNAT Archive format (".xar") | ||
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− | | linear and b-spline | + | | For linear and b-spline transforms. Coordinate system: LPS |
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| [http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf Matlab MAT-File] | | [http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf Matlab MAT-File] | ||
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− | | grid transform | + | | For grid transform. Coordinate system: LPS |
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Revision as of 14:03, 18 May 2014
Home < Documentation < Nightly < SlicerApplication < SupportedDataFormat
For the latest Slicer documentation, visit the read-the-docs. |
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 | For linear and b-spline 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.
- ↑ 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