Repository of brain imaging tools, mostly developed between 2002 and 2013 at the Institute of Computing and at the Neuroimaging Laboratory at Unicamp.

They were originally developed at whatever Linux we used at the labs at the time, and have been updated to compile on updated and stricter environments (CentOS 6/7, Fedora 20-25).

All software in this repository is licensed under the GPL v2.

Directories

• libip image processing library used by IVS and Aftervoxel
• aftervoxel 3D segmentation/visualization tool, GTK+-based GUI
• ivs 3D semi-automatic segmentation tool, implements the differential IFT. The algorithms and this software are described in [Falcao2004]. This directory also contains the dicom2scn conversion tool and a few SCN-related command-line utilities (scntool, scn2ana, ana2scn)
• cppmisc Miscellaneous tools based on the monolithic C++ header I wrote around 2009-2010, including:
  • splitmri (command-line, breaks down multi-echo MRI SCNs)
  • greg (GUI, registration tool)
  • braintag (curvilinear reformatting as per [Bergo2006] and [Bergo2008] and automatic brain segmentation as per [Bergo2007])
  • t2comp (command-line, computes T2 relaxometry regression from a set of multi-echo volumes)
• spineseg Tool for measuring spinal cord atrophy in MRI (performs segmentation with automatic tree pruning [Bergo2007]). The tool is described in [Bergo2012], and its usage is mentioned in [Chevis2013] and [Branco2013]

Most of these tools operate with the SCN 3D image format, which was created internally at Unicamp at the time as a glorified PGM. A description of the format is available as a man page in ivs/man/scn.5

External dependencies:

• Perl 5 (for configuration scripts)
• GTK+ 2.x and its development libraries
• libpng, libjpeg, zlib and their development headers (-devel packages in RedHat-ish distros).
• cppmisc dependencies: bzlib, freetype2

References

• [Bergo2006] F. P. G. Bergo and A. X. Falcão, "Fast and automatic curvilinear reformatting of MR images of the brain for diagnosis of dysplastic lesions," 3rd IEEE International Symposium on Biomedical Imaging: Nano to Macro, 2006., Arlington, VA, 2006, pp. 486-489. https://doi.org/10.1109/ISBI.2006.1624959
• [Bergo2007] F. P. G. Bergo, A. X. Falcão, P. A. V. Miranda and A. X. Falcão, "Automatic Image Segmentation by Tree Pruning", J. Math. Imag. Vision, 29(2), Nov. 2007, pp.141-162. https://doi.org/10.1007/s10851-007-0035-4
• [Bergo2008] F. P. G. Bergo, A. X. Falcão, C. L. Yasuda and F. Cendes, "FCD segmentation using texture asymmetry of MR-T1 images of the brain," 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Paris, 2008, pp. 424-427. https://doi.org/10.1109/ISBI.2008.4541023
• [Bergo2012] F.P.G. Bergo, M.C. França Jr, C.F. Chevis, F. Cendes, "SpineSeg: A Segmentation and Measurement Tool for Evaluation of Spinal Cord Atrophy, CISTI'2012, Jun 2012, Madrid, Spain, vol. 2, pp. 400-403. http://ieeexplore.ieee.org/document/6263238/?tp=&arnumber=6263238
• [Branco2013] L. M. T. Branco, M. de Albuquerque, H.M.T. de Andrade, F.P.G. Bergo, A. Nucci and M.C. França Jr., "Spinal cord atrophy correlates with disease duration and severity in amyotrophic lateral sclerosis", ALS and FT Deg, 15(1-2), Mar. 2014, pp. 93-97. http://dx.doi.org/10.3109/21678421.2013.852589
• [Chevis2013] C.F. Chevis, C.B. da Silva, A. d'Abreu, I. Lopes-Cendes, F. Cendes, F.P.G. Bergo, M.C. França Jr, "Spinal Cord Atrophy Correlates with Disability in Friedreich's Ataxia", Cerebellum, 12(1), Feb 2013, pp. 43-47. https://doi.org/10.1007/s12311-012-0390-6
• [Falcao2004] A. X. Falcão and F. P. G. Bergo, "Interactive volume segmentation with differential image foresting transforms," in IEEE Transactions on Medical Imaging, vol. 23(9), Sep. 2004, pp. 1100-1108. https://doi.org/10.1109/TMI.2004.829335