Difference between revisions of "Documentation/Nightly/SlicerApplication/SupportedDataFormat"

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{{documentation/{{documentation/version}}/slicerapplication-header}}
 
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=File formats supported by Slicer {{documentation/version}}=
 
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{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
 
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|-
 
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!Format
 
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!File Name Extensions
 
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!Read
 
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!Write
 
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!Module
 
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|-
 
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! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Scenes
 
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! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Data|Data]]
 
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|-
 
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| MRML (Medical Reality Markup Language File)
 
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| .mrml
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|MRML file is a xml-formatted text file with scene metadata and pointers to externally stored data files. See [[Documentation/{{documentation/version}}/Developers/MRML|Data Model]]. Coordinate system: RAS
 
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|-
 
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| MRB (Medical Reality Bundle)
 
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| .mrb, .zip
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes (.mrb extension only)
 
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|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
 
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|-
 
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| Slicer 2 Scene
 
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| .xml
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="#f34a33" align="center"|no
 
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| xml-formatted text file with scene metadata and pointers to externally stored data files. Coordinate system: RAS
 
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|-
 
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| Data collections in XNAT Catalog format (".xcat") or XNAT Archive format (".xar")
 
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| .xcat
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="#f34a33" align="center"|no
 
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|
 
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|-
 
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| Data collections in XNAT Archive format (".xar")
 
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| .xar
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="#f34a33" align="center"|no
 
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|
 
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|-
 
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! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Raster Images<br><small>''this includes 2D and 3D images, and more complicated types such as DWI or DTI''</small>
 
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! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]]
 
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|-
 
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| [http://medical.nema.org/ DICOM]
 
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| .dcm ...
 
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|bgcolor="LightGreen" align="center"|yes<ref>For a number of dMRI formats we recommend use of the [[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|DICOM to NRRD converter]] before loading the data into Slicer.</ref>
 
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|bgcolor="LightGreen" align="center"|yes (some data types)<ref>Image volumes, RT structure sets, dose volumes, etc. can be exported using [[Documentation/{{documentation/version}}/Modules/DICOM#DICOM_export|DICOM module's export feature]]. Limited support for writing image volumes in DICOM format is provided by the [[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] module. Support of writing DICOM Segmentation Objects is provided by the [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting extension]]</ref>
 
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|[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]], [[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|DICOMToNRRDConverter]], [[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|CreateDICOMSeries]], [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting extension]]. Coordinate system: LPS (specified by the DICOM standard)
 
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|-
 
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| [http://teem.sourceforge.net/nrrd/format.html NRRD]
 
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| .nrrd, .nhdr
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| Coordinate system: as defined in the file header (usually LPS)
 
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|-
 
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| [http://www.itk.org/Wiki/MetaIO/Documentation MetaImage]
 
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| .mhd, .mha
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| Coordinate system: LPS<ref>According to [http://www.itk.org/Wiki/Proposals:Orientation#Current_ITK_Usage_and_sources_of_confusion MetaIO naming scheme] DICOM 'LPS' direction is 'RAI'.</ref> (AnatomicalOrientation in the file header is ignored)
 
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|-
 
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| [http://www.vtk.org/VTK/img/file-formats.pdf VTK]
 
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| .vtk
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| Coordinate system: LPS
 
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|-
 
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| [http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm Analyze]
 
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| .hdr, .img, .img.gz
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| [http://nifti.nimh.nih.gov/nifti-1/ NifTI]
 
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| .nia, .nii, .nii.gz
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| BMP
 
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| .bmp
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| BioRad
 
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| .pic
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| Brains2
 
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| .mask
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| GIPL
 
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| .gipl .gipl.gz
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| JPEG
 
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| .jpg, .jpeg
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| LSM
 
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| .lsm
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| PNG
 
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| .png
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| Stimulate
 
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| .spr
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| TIFF
 
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| .tif, .tiff
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| MGH-NMR
 
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| .mgz
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| [http://en.wikipedia.org/wiki/MRC_(file_format) MRC] Electron Density
 
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| .mrc, .rec
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Models
 
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! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Models|Models]]
 
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|-
 
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| [http://www.vtk.org/VTK/img/file-formats.pdf VTK Polygonal Data]
 
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| .vtk
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| Coordinate system: RAS
 
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|-
 
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| [http://www.vtk.org/VTK/img/file-formats.pdf VTK XML Polygonal Data]
 
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| .vtp
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| Coordinate system: RAS
 
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|-
 
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| [http://www.vtk.org/VTK/img/file-formats.pdf VTK Unstructured Grid Data]
 
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| .vtk
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| Coordinate system: RAS
 
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|-
 
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| [http://www.vtk.org/VTK/img/file-formats.pdf VTK XML Unstructured Grid Data]
 
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| .vtp
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| Coordinate system: RAS
 
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|-
 
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| STL
 
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| .stl
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| Coordinate system: RAS
 
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|-
 
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| OBJ
 
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| .obj
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| Coordinate system: RAS
 
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|-
 
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| Freesurfer
 
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|  .orig, .inflated, .sphere, .white, .smoothwm, .pial
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="#f34a33" align="center"|no
 
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|
 
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|-
 
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| Others (to be tested)
 
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|  .g, .byu
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="#f34a33" align="center"|no
 
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|
 
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|-
 
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! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Fiducials
 
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! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Markups|Markups]]
 
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|-
 
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| CSV
 
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| .fcsv
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| Coordinate system: RAS
 
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|-
 
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| Text
 
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| .txt
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| Coordinate system: RAS
 
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|-
 
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! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"|Rulers
 
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! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]]
 
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|-
 
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| CSV
 
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| .acsv
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| Coordinate system: RAS
 
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|-
 
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| Text
 
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| .txt
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| Coordinate system: RAS
 
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|-
 
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! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Transforms
 
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! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]]
 
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|-
 
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| [http://www.itk.org/ItkSoftwareGuide.pdf ITK Transform]
 
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| .h5
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| For linear, b-spline, grid (displacement field), thin-plate spline, and composite transforms. Coordinate system: LPS
 
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|-
 
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| [http://www.itk.org/ItkSoftwareGuide.pdf ITK Transform]
 
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| .tfm, .txt
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| For linear, b-spline, and thin-plate spline, and composite transforms. Coordinate system: LPS
 
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|-
 
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| [http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf Matlab MAT-File]
 
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| .mat
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| For linear and b-spline transforms. Coordinate system: LPS
 
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|-
 
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| Displacement field
 
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| .nrrd, .nhdr, .mha, .mhd, .nii, .nii.gz
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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| For grid transform. Coordinate system: LPS
 
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|-
 
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! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Transfer Functions
 
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! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]]
 
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|-
 
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| Volume Rendering properties
 
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| .vp
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| Text
 
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| .txt
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Lookup tables
 
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! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Colors|Colors]]
 
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|-
 
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| [[Documentation/{{documentation/version}}/Modules/Colors#File_format|Text]]
 
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| .txt, .ctbl
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Double Arrays
 
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! scope="col" style="border-top: 1px solid grey;"|
 
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|-
 
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| CSV
 
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| .mcsv
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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|-
 
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| Text
 
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| .txt
 
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|bgcolor="LightGreen" align="center"|yes
 
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|bgcolor="LightGreen" align="center"|yes
 
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|
 
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<references/>
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{{documentation/banner
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| text  = [https://slicer.readthedocs.io/en/latest/user_guide/supported_data_formats.html This page has been moved to read-the-docs.]
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= What if your data is not supported? =
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| background-color = 8FBC8F }}
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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.
 
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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.
 
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Refer to the [http://teem.sourceforge.net/nrrd NRRD format documentation] to see what the keys mean.
 
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=References=
 
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* [http://www.vtk.org/Wiki/ITK_File_Formats ITK File Formats]
 
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{{documentation/{{documentation/version}}/slicerapplication-footer}}
 
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Latest revision as of 16:45, 21 August 2020

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