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Converting MR images to Analyze format

 

This section deals with how to convert these format to Analyze format for use in SPM/Matlab

You may also find it useful to read our small notes about File Formats

 

There are 3 types of MR-image format that needs to be dealt with.

bulletGE Signa format
For images transferred from MRC1 and LXMRT1 using the getmr script
For fMRI and DTI images acquired with the MRC2 scanner but who were stored on the RTIP workstation because of the 1024 images/scan limitations for the MRC2 database

After completed image transfer, your images resides here: <currentdirectory>/<examno>/<seriesno>/I.xyz
Go to each series (cd <examno>/<seriesno>) and type ge2spm -- done!

HINT For later use it may be useful to get information about your series (Patient Name, scan parameters etc.)
Type (after 'cd' to the series) geinfo > info.txt. Now you have a text file, among other things useful when writing the M&M section of your next paper.

NOTE!  getmr, ge2spm and geinfo must be run on ladybird or cicada

Converting MR images to JPEG or AVI
If you want to convert your MR images in Signa format to
=> JPEG    go to the series containing the images to be converted. Type ge2jpg on ladybird or cicada.
=> AVI (Movie)    Start matlab and type ge2avi. Be sure to not choose any I.hdr or I.img files
 
bulletGE Raw format
For fMRI and DTI image data scanned on the MRC1 scanner. Read this pdf document. For DTI, the only difference is that 'epirecon' should be replaced with 'epirecondti'.

NOTE!  Both epirecon and epirecondti must be run on ladybird or cicada
 
bulletDICOM format
For images scanner on the MRC2 scanner or any other modern DICOM conforming MR-system.
On ant only, type dcm to retrieve images from selected MR systems
On any linux host, type 'dcm dcm2spm' to convert your DICOM files to Analyze format. Images are reoriented as 'ge2spm' does, but with the aid of changing parameters to the freeware software xmedcon.

NOTE 1 The dcm script is under development, please report bugs.
NOTE 2 SPM2 (as opposed to earlier versions) support DICOM. However, it is today unclear on exactly how images are oriented if imported directly as DICOM into SPM2. More information to come