Karl-

Thanks for the sample supermosaic. These seem to be very rare, as I have
not seen them before. However, just in case someone else on the SPM mailing
list has these, I will report how to process them with MRIcro.

For those unfamiliar with mosaic images, they are 3D images represented on
a single 2D slice. A 'supermosaic' is a 4D image represented on single 2D
slice. You can convert these with MRIcro, albeit it is a two step process.
You can convert these rare images with MRIcro. The procedure is somewhat
cumbersome, but it does do the trick.

Here is the technique: you first convert the supermosaic into a mosaic, and
then you convert the mosaic to a standard 3D analyze file.

Here are the steps with MRIcro:
  1.) Convert the SuperMosaic to a Mosaic:
     a.) Choose 'Convert foreign to Analyze' from the 'Import' menu.
     b.) In the new window, describe the number of 4D volumes in the mosaic
(e.g. if the supermosaic is 4 volumes wide and 4 volumes high, set both the
mosaic height aand width to 4).
     c.) press select and choose your input file "filename.dcm" and choose
the output name (filename.hdr).
  2.) Convert the Analyze file back to DICOM.
     a.) Select 'Save as [..format..]' from the 'File' menu and press 'Save
DICOM'. You will be asked to select the source file (filename.hdr) and name
the output file 'dfilename.hdr'.
  3.) Convert the mosaic to 3D volumes.
     a.) Choose 'Convert foreign to Analyze' from the 'Import' menu.
     b.) In the new window, describe the number of 3D volumes in the mosaic
(e.g. if the mosaic is 6 slices wide and 6 slices high, set both the mosaic
height aand width to 6).
     c.) press select and choose your input file [*IMPORTANT choose the
*.img" file, not the *.hdr file from the previous step!*] "dfilename.img"
and choose the output name (outname.hdr).

This process will create a giant 3D file - i.e. it will report that you
have only one volume with lots of slices. You will need to adjust the
header to correctly report the number of slices and volumes (e.g. in the
example above, there were 4x4x6x6=288 slices, which are really 4x4=16
volumes and 6x6=36 slices). Once you have modified and saved the header,
you may want to convert the 4D file into a series of 3D files, as SPM likes
to work with 3D files. This is simply a matter of selecting 'Save as
[..format..]' from the file menu and pressing the 'Save [Intel]' button.

-chris

At 13:47 20/11/2001 +0100, Karl Magnus Petersson wrote:
>Hi all,
>
>does anyone know if there is any publically available software that
>converts Dicom SuperMosaic to Analyze format?
>
>All the best.
>
>/karl magnus
>
><<<<<<<<<<<<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>>>>>>>>>>>>
>karl magnus petersson
>Neurocognition of Language Research Group
>Max Planck Institute for Psycholinguistics
>P.O. Box 310, NL-6500 AH Nijmegen, The Netherlands
>
>Cognitive Neurophysiology Research Group R2-01
>Department of Clinical Neuroscience, Karolinska Institutet
>Karolinska Hospital, S-171 76 Stockholm, Sweden
>
>Phone:+31-24-3610658/+46-8-51772039; Mobile:+46-70-5745798;
>Fax: +31-24-3610652/+46-8-344146;
>Email: <mailto:[log in to unmask]>[log in to unmask]
><<<<<<<<<<<<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>>>>>>>>>>>>

__________________________________________
Dr. Chris Rorden
Department of Psychology
University of Nottingham
Nottingham NG7 2RD, UK
Tel: +44 [0]115-951-5294
Fax: +44 [0]115-951-5324
http://www.psychology.nottingham.ac.uk/staff/cr1/