UpdateBot: Nightly -> 4.4

2014-12-25T06:44:04Z

Nightly -> 4.4

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=File formats supported by Slicer {{documentation/version}}=
{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!Format
!File Name Extensions
!Read
!Write
!Module
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Scenes
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Data|Data]]
|-
| MRML (Medical Reality Markup Language File)
| .mrml
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|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
|-
| MRB (Medical Reality Bundle)
| .mrb, .zip
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|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
|bgcolor="LightGreen" align="center"|yes
|bgcolor="#f34a33" align="center"|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
|bgcolor="LightGreen" align="center"|yes
|bgcolor="#f34a33" align="center"|no
|
|-
| Data collections in XNAT Archive format (".xar")
| .xar
|bgcolor="LightGreen" align="center"|yes
|bgcolor="#f34a33" align="center"|no
|
|-
! 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>
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]]
|-
| [http://medical.nema.org/ DICOM]
| .dcm ...
|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>
|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>
|[[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)
|-
| [http://teem.sourceforge.net/nrrd/format.html NRRD]
| .nrrd, .nhdr
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: as defined in the file header (usually LPS)
|-
| [http://www.itk.org/Wiki/MetaIO/Documentation MetaImage]
| .mhd, .mha
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| 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)
|-
| [http://www.vtk.org/VTK/img/file-formats.pdf VTK]
| .vtk
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: LPS
|-
| [http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm Analyze]
| .hdr, .img, .img.gz
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| [http://nifti.nimh.nih.gov/nifti-1/ NifTI]
| .nia, .nii, .nii.gz
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| BMP
| .bmp
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| BioRad
| .pic
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| Brains2
| .mask
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| GIPL
| .gipl .gipl.gz
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| JPEG
| .jpg, .jpeg
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| LSM
| .lsm
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| PNG
| .png
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| Stimulate
| .spr
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| TIFF
| .tif, .tiff
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| MGH-NMR
| .mgz
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| [http://en.wikipedia.org/wiki/MRC_(file_format) MRC] Electron Density
| .mrc, .rec
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Models
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Models|Models]]
|-
| [http://www.vtk.org/VTK/img/file-formats.pdf VTK Polygonal Data]
| .vtk
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
| [http://www.vtk.org/VTK/img/file-formats.pdf VTK XML Polygonal Data]
| .vtp
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
| STL
| .stl
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
| OBJ
| .obj
|bgcolor="LightGreen" align="center"|yes
|bgcolor="#f34a33" align="center"|no
|
|-
| Freesurfer
| .orig, .inflated, .sphere, .white, .smoothwm, .pial
|bgcolor="LightGreen" align="center"|yes
|bgcolor="#f34a33" align="center"|no
|
|-
| Others (to be tested)
| .g, .byu
|bgcolor="LightGreen" align="center"|yes
|bgcolor="#f34a33" align="center"|no
|
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Fiducials
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Markups|Markups]]
|-
| CSV
| .fcsv
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
| Text
| .txt
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"|Rulers
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]]
|-
| CSV
| .acsv
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
| Text
| .txt
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Transforms
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]]
|-
| [http://www.itk.org/ItkSoftwareGuide.pdf ITK Transform]
| .tfm, .txt
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| For linear and b-spline transforms. Coordinate system: LPS
|-
| [http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf Matlab MAT-File]
| .mat
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| For linear and b-spline transforms. Coordinate system: LPS
|-
| Displacement field
| .nrrd, .nhdr, .mha, .mhd, .nii, .nii.gz
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| For grid transform. Coordinate system: LPS
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Transfer Functions
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]]
|-
| Volume Rendering properties
| .vp
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| Text
| .txt
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Lookup tables
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Colors|Colors]]
|-
| [[Documentation/{{documentation/version}}/Modules/Colors#File_format|Text]]
| .txt, .ctbl
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Double Arrays
! scope="col" style="border-top: 1px solid grey;"|
|-
| CSV
| .mcsv
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| Text
| .txt
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|}

<references/>

=References=
* [http://www.vtk.org/Wiki/ITK_File_Formats ITK File Formats]


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Documentation/4.4/SlicerApplication/SupportedDataFormat - Revision history

UpdateBot: Nightly -> 4.4