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Yes, but what about Mayo ANALYZE, or Matlab?

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Q13. Yes, but what about Mayo ANALYZE, or Matlab?
Mike Beauchamp of the NIMH has written the following potentially useful documents:

How to make AFNI and Mayo ANALYZE interoperate.
How to use AFNI datasets in a Matlab program.
A more recent description of using AFNI datasets in Matlab [Ziad Saad].
How to use program 3dDeconvolve to analyze an FMRI time series with multiple linear regression.

In addition, to3d can now read ANALYZE .hdr/.img file pairs without special 3D: encoding (see the bottom part of Q12, above). Since MRI data in ANALYZE format seems mostly to be stored in 3D arrays, you will generally have a lot of file pairs for an EPI run. You have to use -time:zt to specify the time axis. ANALYZE .hdr files contain the voxel spacings, so you shouldn't have to change those parameters. However, ANALYZE .hdr files do not reliably contain the image orientation or spatial offset, so you have to enter this information manually into to3d.

The new [29 Nov 2001] program 3dAFNItoANALYZE will write the write each 3D sub-brick from an AFNI dataset to an ANALYZE file pair. This capability should make it not-too-painful to use AFNI and SPM together.

[Answer last changed 30 Nov 2001]

This FAQ applies to: Any version.

Created by Robert Cox
Last modified 2005-07-31 10:30