Hi,

We've been having trouble getting CT images into Analyze format using
MRIcro and rotating them afterwards. The 'Convert Foreign to Analyze'
function and the conversion wizard both produce seemingly random patterns
of black, grey and white dots. We think this is probably due at least in
part to our images(75 files) not all being exactly the same size (they
range from 520-524KB), but we're not sure if there are other problems.

I've tried two ways of getting around this:

1) We ran the files through MRIconvert, which created 25 .hdr/.img pairs of
files, each containing three slices. We then ran that through the MRIcro
conversion wizard, which then created a single .hdr/.img pair.

2) We also tried using dicom2 to convert our .dcm files into dicom files
that were all the same size. That seemed to work, and MRIcro could then
stack them into a single volume, creating a single .hdr/.img pair.

Problems:
a) the image file created in both cases was 38,400KB in size, making it
very slow to work with.
Questions: Is there a more straightforward way to do this conversion? Is
there a way to make the resultant file smaller? Are we losing any
information in these 2 step processes?

b) we need to change the pitch value of this volume, and if the xbars are
not set exactly right during Free Rotate we get images that move up or down
across the screen as we scroll through the volume.
Question: Is there a way of determining if the xbars are centered
correctly? Otherwise, we have to use trial and error and keep moving them
around until things work.

Any advice you can give would be appreciated -- thank you very much for
your help!

Esther Lee
MRRI