Amira Import

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This document walks you through about how to import raw data form acquired from the scanner.

Import from Robarts Imaging Micro-CT Data

Normally, on the CD/DVD you acquired from them, make sure you also obtain these information from them:

Voxel size: eg. 0.153884mm * 0.153884mm * 0.153884mm, given in terms of the voxel size. The dimension of the image: eg. 470 * 470 * 650 Data Type: eg. Short (16bit) Data Endian: eg. little endian

Here are the steps: read them CAREFULLY!

Amira 5.0+ have some seriously problem loading a SERIES of slice based raw data.This means, if you load 500 .dat file in Amira 5.0, they will treat them as individual file and load them one at a time. if you enjoy clicking "okay" 600+ times and playing with 600+ green data modules, go ahead and use Amira 5.0. This is the ONLY reason why I kept verion 4 around. Amira version 4 is able to actually load up all the individual .dat raw data file by combining them together and ask for the parameter in the end instead of breaking them up. So far, I have not found work around for this yet.

By the way, VFF file is still having some kind of problem when loaded. I would not recommand using that format for the moment. DICOM is the most highly recommended format to play with and the 2nd best is the RAW data

Major Contacts at Robarts

Any more specific questions regarding data should be directed to either Joseph Umoh (micro CT, preclinical scanning) or Joe Gati (fMRI).