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

From Slicer Wiki
Jump to: navigation, search
m
(Replaced content with "<noinclude>{{documentation/versioncheck}} </noinclude> {{documentation/banner | text = [https://slicer.readthedocs.io/en/latest/user_guide/supported_data_formats.html Th...")
Tags: 2017 source edit, Replaced
 
(9 intermediate revisions by 3 users not shown)
Line 1: Line 1:
<noinclude>{{documentation/versioncheck}}</noinclude>
+
<noinclude>{{documentation/versioncheck}}
<!-- ---------------------------- -->
+
</noinclude>
{{documentation/{{documentation/version}}/slicerapplication-header}}
 
<!-- ---------------------------- -->
 
=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.  [[Documentation/{{documentation/version}}/Developers/MRML|Data Model]]
 
|-
 
| 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 (orientation information 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/>
+
{{documentation/banner
 
+
| text  = [https://slicer.readthedocs.io/en/latest/user_guide/supported_data_formats.html This page has been moved to read-the-docs.]
=References=
+
| background-color = 8FBC8F }}
* [http://www.vtk.org/Wiki/ITK_File_Formats ITK File Formats]
 
 
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/slicerapplication-footer}}
 
<!-- ---------------------------- -->
 

Latest revision as of 16:45, 21 August 2020

Home < Documentation < Nightly < SlicerApplication < SupportedDataFormat