Re: viewing data that was analyzed by the NIS/AIR package in afni

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Posted by bob cox on November 12, 2002 at 13:41:01:

In Reply to: viewing data that was analyzed by the NIS/AIR package in afni posted by Trin on November 12, 2002 at 10:30:43:

If you have a recent version of AFNI, it can directly view .hdr/.img (ANALYZE format) file pairs. This feature was added about 01 Sep 2002. The main drawback of this feature is that ANALYZE files don't contain information about the orientation of the volumes. As a result, AFNI guesses that they are oriented as axial slices, with the x-axis being L-R, y axis as P-A, and z axis as I-S. If this is not correct, then using the Image "Axial", "Sagittal", and "Coronal" buttons will open the wrong view. You can get around this problem by setting the environment variable AFNI_ANALYZE_ORIENT to specify the correct orientation. The details on how to do this are in the file README.environment.

If you do want to convert ANALYZE files to AFNI format, the program to use is to3d; for example:

  to3d fred.hdr

will present you with a GUI for converting a single 3D file to an AFNI dataset. If you need to convert multiple 3D files, or a 4D file, to an AFNI 3D+time dataset, then you'll need to read the documentation for to3d. Or possible use one of the AFNI Howtos as a tutorial on this subject.

However, to start with, download the latest AFNI version, then fire it up in the directory with the files you want to peruse, and see what happens. That may be enough for your immediate purposes.

bob cox

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