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

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(Added info on coordinate systems)
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|bgcolor="LightGreen" align="center"|yes
 
|bgcolor="LightGreen" align="center"|yes
 
|bgcolor="LightGreen" align="center"|yes (.mrb extension only)
 
|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.
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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
 
|-
 
|-
 
| Slicer 2 Scene
 
| Slicer 2 Scene
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|bgcolor="#f34a33" align="center"|no
 
|bgcolor="#f34a33" align="center"|no
 
| xml-formatted text file with scene metadata and pointers to externally stored data files.
 
| 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")
 
| Data collections in XNAT Catalog format (".xcat") or XNAT Archive format (".xar")
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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>
 
|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>
 
|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]]
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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)
 
|-
 
|-
 
| [http://teem.sourceforge.net/nrrd/format.html NRRD]
 
| [http://teem.sourceforge.net/nrrd/format.html NRRD]
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|bgcolor="LightGreen" align="center"|yes
 
|bgcolor="LightGreen" align="center"|yes
 
|bgcolor="LightGreen" align="center"|yes
 
|bgcolor="LightGreen" align="center"|yes
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|
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| Coordinate system: as defined in the file header (usually LPS)
 
|-
 
|-
 
| [http://www.itk.org/Wiki/MetaIO/Documentation MetaImage]
 
| [http://www.itk.org/Wiki/MetaIO/Documentation MetaImage]
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|bgcolor="LightGreen" align="center"|yes
 
|bgcolor="LightGreen" align="center"|yes
 
|bgcolor="LightGreen" align="center"|yes
 
|bgcolor="LightGreen" align="center"|yes
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|
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| Coordinate system: LPS (orientation information in the file header is ignored)
 
|-
 
|-
 
| [http://www.vtk.org/VTK/img/file-formats.pdf VTK]
 
| [http://www.vtk.org/VTK/img/file-formats.pdf VTK]
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|bgcolor="LightGreen" align="center"|yes
 
|bgcolor="LightGreen" align="center"|yes
 
|bgcolor="LightGreen" align="center"|yes
 
|bgcolor="LightGreen" align="center"|yes
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|
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| Coordinate system: LPS
 
|-
 
|-
 
| [http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm Analyze]
 
| [http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm Analyze]
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|bgcolor="LightGreen" align="center"|yes
 
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|
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| Coordinate system: RAS
 
|-
 
|-
 
| [http://www.vtk.org/VTK/img/file-formats.pdf VTK XML Polygonal Data]
 
| [http://www.vtk.org/VTK/img/file-formats.pdf VTK XML Polygonal Data]
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| Coordinate system: RAS
 
|-
 
|-
 
| STL
 
| STL
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| Coordinate system: RAS
 
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| Text
 
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| Coordinate system: RAS
 
|-
 
|-
 
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"|Rulers
 
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"|Rulers
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| Coordinate system: RAS
 
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|-
 
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Transforms
 
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Transforms
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| linear and b-spline transform
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| linear and b-spline transform; Coordinate system: LPS
 
|-
 
|-
 
| [http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf Matlab MAT-File]
 
| [http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf Matlab MAT-File]
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| linear and b-spline transform; Coordinate system: LPS
 
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| Displacement field
 
| Displacement field
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| grid transform
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| grid transform; Coordinate system: LPS
 
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|-
 
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Transfer Functions
 
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Transfer Functions

Revision as of 14:01, 18 May 2014

Home < Documentation < Nightly < SlicerApplication < SupportedDataFormat


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


File formats supported by Slicer Nightly

Format File Name Extensions Read Write Module
Scenes Data
MRML (Medical Reality Markup Language File) .mrml yes yes MRML file is a xml-formatted text file with scene metadata and pointers to externally stored data files. Data Model
MRB (Medical Reality Bundle) .mrb, .zip yes 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 yes 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 yes no
Data collections in XNAT Archive format (".xar") .xar yes no
Raster Images
this includes 2D and 3D images, and more complicated types such as DWI or DTI 		Volumes
DICOM .dcm ... yes[1] no[2] DICOM, DICOMToNRRDConverter, CreateDICOMSeries, Reporting extension. Coordinate system: LPS (specified by the DICOM standard)
NRRD .nrrd, .nhdr yes yes Coordinate system: as defined in the file header (usually LPS)
MetaImage .mhd, .mha yes yes Coordinate system: LPS (orientation information in the file header is ignored)
VTK .vtk yes yes Coordinate system: LPS
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
MRC Electron Density .mrc, .rec yes yes
Models Models
VTK Polygonal Data .vtk yes yes Coordinate system: RAS
VTK XML Polygonal Data .vtp yes yes Coordinate system: RAS
STL .stl yes yes coordinate system: RAS
OBJ .obj yes no
Freesurfer .orig, .inflated, .sphere, .white, .smoothwm, .pial yes no
Others (to be tested) .g, .byu yes no
Fiducials Markups
CSV .fcsv yes yes Coordinate system: RAS
Text .txt yes yes Coordinate system: RAS
Rulers Annotations
CSV .acsv yes yes Coordinate system: RAS
Text .txt yes yes Coordinate system: RAS
Transforms Transforms
ITK Transform .tfm, .txt yes yes linear and b-spline transform; Coordinate system: LPS
Matlab MAT-File .mat yes yes linear and b-spline transform; Coordinate system: LPS
Displacement field .nrrd, .nhdr, .mha, .mhd, .nii, .nii.gz yes yes grid transform; Coordinate system: LPS
Transfer Functions Volume Rendering
Volume Rendering properties .vp yes yes
Text .txt yes yes
Lookup tables Colors
Text .txt, .ctbl yes yes
Double Arrays
CSV .mcsv yes yes
Text .txt yes yes
  1. ↑ For a number of dMRI formats we recommend use of the DICOM to NRRD converter before loading the data into Slicer.
  2. ↑ Limited support for writing image volumes in DICOM format is provided by the Create DICOM Series module. Support of writing DICOM Segmentation Objects is provided by the Reporting extension

References

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