DICOM Image Viewing & Conversion to Analyze/SPM

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Conclusion

OsiriX (Mac OS X only) and eFilmLite are the best GUI applications for browsing through raw MRI DICOM images. They provide simple methods to navigate between images and series, show images as thumbnail tiles, view header data, and adjust image settings.

MRIConvert was the only tool found that correctly converts DICOM images to Analyze/SPM format. A useful feature is the ability to automatically perform the conversion on several directories of files, without any user input.

MRIcro is the best GUI application for viewing images in Analyze/SPM format. It has slice viewer tools and other useful features to allow for manipulation of the image.

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listing of more viewers... http://www.mail-archive.com/morphmet%40morphometrics.org/msg01108.html

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Viewers

Viewer Software Lists
http://www.refindia.net/ref/activities/onlinelectures/diyprimer_dicorm/part2.htm
http://www.sph.sc.edu/comd/rorden/dicom.html

1. OsiriX (Sid's computer)
   Pro:
   • Has image browser capability!
   • Sid has no problems using it
   • Ability to view header data
   • Easy to adjust image settings
   Con:
   • For Mac OS X only
2. eFilmLite (provided with MRI scan data)
   Pro:
   • Ability to view header data as image overlay
   • Easy navigation between patients, studies, series and images
   • Easy to adjust image settings (brightness/contrast)
   • Ability to view as 3D image
   • Measurement feature
   Con:
   • No image browser capability
3. ImageJ (http://rsb.info.nih.gov/ij/)
   Pro:
   • GUI and toolkit, open source
   • Ability to open entire series
   • Ability to adjust image settings
   • Measurement feature
   Con:
   • No image browser capability
4. ezDICOM (http://www.sph.sc.edu/comd/rorden/ezdicom.html)
   Pro:
   • Simple standalone viewer GUI and command line app, with source
   • Can open multiple images in one directory (eg. one series)
   Con:
   • No image browser capability
   • Cannot open all images in multiple directories (eg. multiple series)
   • DICOM->Analyze converter batch converts, but performs 1:1 image conversion (does not combine multiple DICOM into a single Analyze image)
5. MRIcro (http://www.sph.sc.edu/comd/rorden/mricro.html)
   Pro:
   • Good Analyze image viewer
   • Slice viewer for Analyze image
   • Lots of useful GUI features (view header info, adjust image settings)
   • DICOM->Analyze converter capability
   Con:
   • No image browser capability
   • Does not recognize raw MRI image format
6. MRIcron (http://www.sph.sc.edu/comd/rorden/mricron/)
   Pro:
   • DICOM->Analyze converter beta software
   • Open source version of MRIcon
   Con:
   • No image browser capability
   • Not as usable as MRIcon
7. 3D-DOCTOR (http://www.ablesw.com/3d-doctor/)
   Pro:
   • Creation of polygonal mesh models from DICOM through manual tracing and automatic threshold segmentation
   Con:
   • No image browser capability
   • Poor quality result
   • High learning curve
   • Using trial version does not allow saving
8. Osiris (http://www.dim.hcuge.ch/osiris/01_Osiris_Presentation_EN.htm)
   Con:
   • Did not recognize format -- raw image required manual entry of dimensions, etc.

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Conversion to Analyze/SPM Image

1. MRIConvert (http://lcni.uoregon.edu/~jolinda/MRIConvert/)
   1. Choose input/output directories
   2. Select SPM Analyze
   3. Convert all
   Pro:
   • Batch conversion
   • Images correctly ordered
   • Directories labelled by series name
   • Command line version
   • Does not require any manual entry of settings
   Con:
   • No viewer capabilities
2. MRIcro (http://www.sph.sc.edu/comd/rorden/mricro.html)
   1. Import -> Convert foreign to to Analyze...
      • number of files
      • slice increment=1
      • volume increment=0
      • volumes=1
      • mosaic rows=1
      • mosaic columns=1
   2. Select first DICOM image
   3. Save .hdr file
   Pro: Con:
   • Converter converts only one Analyze file at a time and requires user to indicate settings (eg. # files)
   • Images not correctly ordered
3. MRIcron (http://www.sph.sc.edu/comd/rorden/mricron/)
   Pro:
   • DICOM->Analyze converter beta software
   Con:
   • Converter enabled only after modification of .ini file
4. ezDICOM (http://www.sph.sc.edu/comd/rorden/ezdicom.html)
   Con:
   • DICOM->Analyze converter batch converts, but performs 1:1 image conversion (does not combine multiple DICOM into a single Analyze image)

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