Status of Analyze 7.5 file format support

Engineering
1

Hi all,

Now that the itkAnalyzeImageIO class is gone in ITK git master, I’m looking at updating my app (which uses this class).

First question: why was this class deprecated and removed anyway?

Anyway, I’ve been looking at using itkNiftiImageIO instead, and have read through the class. I have some trivial fixes here:

http://review.source.kitware.com/23082
http://review.source.kitware.com/23083
http://review.source.kitware.com/23084
http://review.source.kitware.com/23085

These are ready to merge IMHO.

But bigger problems I’d like to discuss, because I’m not sure of the solutions…:

  1. What are the desired semantics of SetImageIOMetadataFromNIfTI() exactly? It currently populates the metadata dictionary with data from the ‘nifti_1_header’, which is literally the first 348 bytes of the file. I’m thinking it might be better to populate it from ‘nifti_image’ instead, which is largely the same, but after some processing by nifti_convert_nhdr2nim(). For example, line 3765 forces the ‘qform_code’ field to 0 for Analyze 7.5 files, since that offset in the header had a different meaning pre-NIfTI. By using the literal header fields, SetImageIOMetadataFromNIfTI() is currently providing garbage sform and qform values for Analyze files. My WIP proposed fix is here:

http://review.source.kitware.com/23086

Which basically uses the data from ‘nifti_image’ instead. A handful of fields need a little manipulation to get back in the same format. I basically did what nifti_convert_nim2nhdr() does.

As a bonus, this removes extra file i/o by eliminating the nifti_read_header() call.

  1. There doesn’t seem to be a good way to query if the file read was Analyze 7.5 or NIfTI. I’d like to distinguish because my app gives a warning when Analyze is opened (to ween users off this format). My above patch adds the ‘nifti_type’ field to the metadata to make that info available.

  2. the ‘USE_VERY_VERBOSE_NIFTI_DEBUGGING’ option (that’s not compiled by default) is broken. When enabled, several tests fail with invalid memory access. I didn’t investigate much here…

Thanks,

Sean

2

Thanks for the patches, Sean. @hjmjohnson is the expert on this issue.