MRI images

These reconstructions have been presented in The 13th Conference of the Bioimaging Society of Japan, as poster titled "Three-dimensional Reconstruction from MRI data using DeltaViewer" by Masaaki Wada, Nobuko Katagiri, Yasuhide Shigematsu, Sachiko Fujihara, Chiaki Nishibori, Chisen Takeuchi, Shiori Hashimoto, Akio Horii and Yasuo Katagiri. Click on each image to see a larger picture.

The original MRI data of my brain (!) were sampled at Tokyo Women's Medical University Hospital on September 1, 2004 by Toshiba Excelart 1.5T MRI scanner using FE3D sequence with parameters TR=25 and TE=6.8. There are 160 cross sectional images of size 512 x 512 at 0.5 mm per pixel relolution. The spacing between slices is 1 mm. We are very much grateful to Prof. Yuko Ono and Chief Engineer Shigetoshi Yoshida for their cooperation in acquiring the MRI data.

The format of the scanned digital images was DICOM, a popular image file format among medical applications. To use the digital data by DeltaViewer, we first converted them into TIFF images using OsiriX, a free DICOM viewer. The top left image below is one of such images. We then read those TIFF images one by one into Photoshop and traced the region corresponding to neurons manually (top right), saved the selection into channel named "a", and saved the results as Photoshop psd files. This process takes a long time. Once we have processed all cross sections this way, it is now easy by using Photoshop's "Batch" function to produce a stack of images where outside of selection is colored 20% yellow (bottom left) and another stack of images where outside of the selection is just plain black (bottom right). You may read one of these stacks, or a combination of both, into DeltaViewer and obtain reconstructions like the ones shown at the top of this page.

I was not careful enough about the orientation; the final reconstruction seems to be the mirror image of the real thing. :)


These data may be used for research and education purposes in any way without reference to the source. However, secondary distribution of these data is not allowed without permission.