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Friday, June 20, 2008

BrainVISA Anatomist MRIcro NeuroImage file format

BrainVISA is a software, which embodies an image processing factory. A simple control panel allows the user to trigger some sequences of treatments on series of images. These treatments are performed by calls to command lines provided by different laboratories. These command lines, hence, are the building blocks on which are built the assembly lines of the factory.

La plate-forme BrainVISA est dédiée à l’organisation et au traitement de données de neuro-imagerie (IRM, EEG, MEG, EEG ...) alors que le logiciel Anatomist permet de visualiser et manipuler cet ensemble de données (changement de système de coordonnées, fusion et superposition d’objets ...).

et un autre domaine publique : MRIcro.


(2008/06/10) brainvisa/anatomist version 3.1 is available.

sur la multimodalité:

MRIcro permet d'afficher les images issues de logiciels d'imagerie médicale cérébrale (SPM inclus), et ce afin de pouvoir les analyser plus simplement. Vous pourrez avoir accès à toutes les informations nécessaires (incluses dans les fichiers source) : dimensions, vue en coupe, vue 3D, rotation, etc. L'application dispose également d'un module de modification du contraste par région (sélectionnez la zone que vous voulez modifier), d'une option de comparaison de deux documents, etc. Un tutorial complet est disponible sur le site de l'auteur.

pour mac:

file format converters:

DCM2NII attempts to convert images from the proprietary scanner format to the NIfTI format used by FSL, SPM5, MRIcron and many other brain imaging tools. NIfTI is a modern incarnation of the Analyze format, but includes important information like the orientation of the image. DCM2NII is a stand-alone program that is distributed with MRIcron. It is natively compiled for Windows, Linux x86, Mac OSX PPC and Mac OSX x86.

Each manufacturer has interpretted the DICOM data standard a bit differently. Therefore, you may want to test several programs to see which one is best suited for your data
  1. LONI Debabeler is a Java applet that can run on just about any computer. It can also read a number of medical imaging formats. Another nice feature is that it reorients the raw data to be approximately aligned with the nearest orthogonal orientation (i.e. coronal and sagittal scans are resliced along the axial plane).
  2. SPM5 includes a DICOM to NIfTI covnerter that works particularly well for Siemens data (requires Matlab).
  3. dicom2nifti is a Matlab script for converting DICOM to NIfTI (requires Matlab and the Matlab Image Processing Toolbox). [an alternative version is described here.]
  4. xmedcon offers limited NIfTI writing support for many image formats. It uses the niftilib tools, which look very useful.
  5. MRIconvert is a popular converter for Windows and Linux.
  6. dinifti looks useful.
  7. Here is a script that uses dicom2 and FSL to convert DICOM images to NIfTI.
  8. XMedCon includes the ability to convert between Acr/Nema 2.0, Analyze (SPM), Concorde/µPET, DICOM 3.0, CTI ECAT 6/7, NIfTI-1, InterFile3.3 and PNG or Gif87a/89a formats, as well as an elegant image viewer.
  9. r2aGUI Converts Philips PAR/REC images to NIfTI. Requires Matlab.
  10. The latest Philips Achieva research tools software can now directly produce (4D) nifti files This is a great alternative to using dcm2nii or r2agui. Kudos to Philips for directly supporting the NIfTI format.

Platforms, limitations, alternatives: MRIcro supports the Windows and Linux platforms. Here is a short list of some freeware Analyze format image viewers that are currently available for the Windows PC (for a list of Linux software, see the MRIcro for Linux web page. A more extensive list of DICOM viewers for Unix, Macintosh and PCs is available at my DICOM page):
Viewer Platforms Formats [Notes]
SPM Unix/Windows NT Analyze [requires Matlab]
Slice Overlay Unix/Windows NT Analyze [requires Matlab]
SPMwin Windows Analyze
ACTIV 2000 Windows Analyze/DICOM/GE/GIS/PAR/Siemens
Medal Windows Analyze/DICOM
etdips Windows Analyze/DICOM/TIFF
Spamalize Unix/Windows/Macintosh Analyze/GE/TIFF [requires IDL]
AMIDE Unix/Windows Analyze/DICOM/ECAT6/Interfile
XMedCon Unix/Windows Analyze/DICOM/ECAT6/Interfile
ezDICOM Windows Analyze/ECAT/Interfile/Siemens/Picker/GE/DICOM/VoxBo
ImageJ w. Analyze plugin Unix/Windows/Macintosh Analyze/DICOM
Space Windows Analyze/VOL [beta release]

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