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="#f34a33" align="center"|no<ref>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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| 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="#f34a33" align="center"|no
 
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|
 
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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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| .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 and b-spline 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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|}
 
  
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<references/>
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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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=References=
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| background-color = 8FBC8F }}
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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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