Difference between revisions of "Documentation/4.0/SlicerApplication/SupportedDataFormat"

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(Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887)
 
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<noinclude>{{documentation/versioncheck}}</noinclude>
 
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{{documentation/{{documentation/version}}/slicerapplication-header}}
 
{{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;"
−
=Volumes=
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|-
−
*NRRD (.nrrd)
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!Format
−
*NRRD (.nhdr)
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!Extensions
−
*MetaImage (.mhd)
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!Read
−
*MetaImage (.mha)
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!Write
−
*VTK (.vtk)
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!Module
−
*Analyze (.hdr)
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|-
−
*Analyze (.img)
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! scope="col" colspan="4" style="border-bottom: 1px solid grey;"| Scenes
−
*Analyze (.img.gz)
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! scope="col"| [[Documentation/{{documentation/version}}/Modules/Data|Data]]
−
*BMP (.bmp, .BMP)
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|-
−
*BioRad (.pic)
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| MRML
−
*Brains2 (.mask)
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| .mrml
−
*GIPL (.gipl, .gipl.gz)
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|bgcolor="LightGreen" align="center"|yes
−
*JPEG (.jpg, .jpeg, .JPG, .JPEG)
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|bgcolor="LightGreen" align="center"|yes
−
*LSM (.lms, .LSM)
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|[[Documentation/{{documentation/version}}/Developers/MRML|Data Model]]
−
*NifTI (.nia)
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|-
−
*NifTI (.nii, .nii.gz)
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! scope="col" colspan="4" style="border-bottom: 1px solid grey;"| Raster Images<br><small>''this includes 2D and 3D images, and more complicated types such as DWI or DTI''</small>
−
*PNG (.png, .PNG)
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! scope="col"| [[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]]
−
*Stimulate (.spr)
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|-
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*TIFF (.tiff, .tif, .TIFF, .TIF)
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| [http://medical.nema.org/ DICOM]
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*MGH-NMR (.mgz)
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| .dcm ...
−
 
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|bgcolor="LightGreen" align="center"|yes
−
=Models=
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|bgcolor="#f34a33" align="center"|no<ref>Limited support for writing image volumes in DICOM format is provided by the [[Documentation/4.0/Modules/ImageReadDicomWrite|Create DICOM Series]] module</ref>
−
*Poly Data (.vtk)
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|[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]]
−
*XML Poly Data (.vtp)
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|-
−
*STL (.stl)
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| [http://teem.sourceforge.net/nrrd/format.html NRRD]
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*OBJ (.obj)
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| .nrrd, .nhdr
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|bgcolor="LightGreen" align="center"|yes
−
=Fiducials=
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|bgcolor="LightGreen" align="center"|yes
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*Fiducial List CSV (.fcsv)
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|
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*Text (.txt)
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|-
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=Transforms=
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| [http://www.itk.org/Wiki/MetaIO/Documentation MetaImage]
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*Transform (.tfm and .mat) (ITK v3 Transform format documented [http://www.itk.org/ItkSoftwareGuide.pdf here])
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| .mhd, .mha
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*Text (.txt)
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|bgcolor="LightGreen" align="center"|yes
−
 
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|bgcolor="LightGreen" align="center"|yes
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=Transfer functions=
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|
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*Volume Rendering properties (.vp)
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|-
−
 
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| [http://www.vtk.org/VTK/img/file-formats.pdf VTK]
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| .vtk
 +
|bgcolor="LightGreen" align="center"|yes
 +
|bgcolor="LightGreen" align="center"|yes
 +
|
 +
|-
 +
| [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
 +
|
 +
|-
 +
! scope="col" colspan="4" style="border-bottom: 1px solid grey;"| Models
 +
! scope="col"| [[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
 +
|
 +
|-
 +
| [http://www.vtk.org/VTK/img/file-formats.pdf VTK XML Polygonal Data]
 +
| .vtp
 +
|bgcolor="LightGreen" align="center"|yes
 +
|bgcolor="LightGreen" align="center"|yes
 +
|
 +
|-
 +
| STL
 +
| .stl
 +
|bgcolor="LightGreen" align="center"|yes
 +
|bgcolor="LightGreen" align="center"|yes
 +
|
 +
|-
 +
| OBJ
 +
| .obj
 +
|bgcolor="LightGreen" align="center"|yes
 +
|bgcolor="#f34a33" align="center"|no
 +
|
 +
|-
 +
| Others (to be tested)
 +
|  .g, .byu, .orig, .inflated, .sphere, .white, .smoothwm, .pial
 +
|bgcolor="LightGreen" align="center"|yes
 +
|bgcolor="#f34a33" align="center"|no
 +
|
 +
|-
 +
! scope="col" colspan="4" style="border-bottom: 1px solid grey;"| Fiducials
 +
! scope="col"| [[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]]
 +
|-
 +
| CSV
 +
| .fcsv
 +
|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;"| Transforms
 +
! scope="col"| [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]]
 +
|-
 +
| [http://www.itk.org/ItkSoftwareGuide.pdf Transform]
 +
| .tfm, .mat
 +
|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;"| Transfer Functions
 +
! scope="col"| [[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;"| Lookup tables
 +
! scope="col"| [[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
 +
|
 +
|}
 +
<references/>
 
=References=
 
=References=
 
* [http://www.vtk.org/Wiki/ITK_File_Formats ITK File Formats]
 
* [http://www.vtk.org/Wiki/ITK_File_Formats ITK File Formats]

Latest revision as of 07:36, 14 June 2013

Home < Documentation < 4.0 < SlicerApplication < SupportedDataFormat


For the latest Slicer documentation, visit the read-the-docs.


File formats supported by Slicer 4.0

Format Extensions Read Write Module
Scenes Data
MRML .mrml yes yes Data Model
Raster Images
this includes 2D and 3D images, and more complicated types such as DWI or DTI 		Volumes
DICOM .dcm ... yes no[1] DICOM
NRRD .nrrd, .nhdr yes yes
MetaImage .mhd, .mha yes yes
VTK .vtk yes yes
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
Models Models
VTK Polygonal Data .vtk yes yes
VTK XML Polygonal Data .vtp yes yes
STL .stl yes yes
OBJ .obj yes no
Others (to be tested) .g, .byu, .orig, .inflated, .sphere, .white, .smoothwm, .pial yes no
Fiducials Annotations
CSV .fcsv yes yes
Text .txt yes yes
Transforms Transforms
Transform .tfm, .mat yes yes
Text .txt yes yes
Transfer Functions Volume Rendering
Volume Rendering properties .vp yes yes
Text .txt yes yes
Lookup tables Colors
Text .txt, .ctbl yes yes
  1. ↑ Limited support for writing image volumes in DICOM format is provided by the Create DICOM Series module

References

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