[Insight-users] strncpy problem in itkAnalyzeImageIO.cxx

[Hans Johnson]

Luis,

We've had some discussions to that end here at Iowa.  This is quite
difficult, because the SPM format has no "Magic Identifier" that
distinguishes it from compliant Analyze images.  We will investigate
this when we start the implementation of the NIfTY file format.

Hans


On Mon, 2004-06-21 at 11:28, Luis Ibanez wrote:
> Jill, Hans,
> 
> The changes of memcpy/stncpy in itkAnalyzeImageIO
> have been reverted.
> 
> Should we have a SPMImageIO class in order to solve
> this deviation of format ?
> 
> This eventual new class could probably derive from
> AnalyzeImageIO...
> 
> 
> 
>      Luis
> 
> 
> --------------------
> Hans Johnson wrote:
> 
> > Jill,
> > 
> > The header Meta-Data information is not handled implicitly by ITK, you
> > must explicitly handle that with your own code.  There is a mechanism to
> > attach Meta-Data to any ITK object, but the application programmer must
> > judiciously propogate that information through the pipelines to make
> > sure that it is preserved.  This may seem like a hassle, but it is
> > actually a well thought out design decision. 
> > 
> > This method is not very safe.  The std::string temp is not gaunteed to
> > have 10 elements in it, and this will cause a segmentation fault on
> > non-spm image types.  The "10" in the strncpy(dest,sorce,10) specifies
> > the following behavior: "copy source characters into dest until either a
> > '\0' is reached or 10 characters have been copied".  
> > 
> > For spm formatted images the originator field is not treated as a
> > character array (if temp=[0 128 0 128 0 64 0 0 0 0], that is 23
> > characters in it).  To use the SPM format you must create an 8-bit
> > unsigned array with 10 elements, and memcpy that into the originator
> > feild.  This would require a new metadata tag to be created and keyed
> > off of.
> > 
> > The SPM file format is a particularly nasty deviation from the Analyze
> > 7.5 file format, and causes many people lots of headaches.  If you are
> > needing SPM, then you are probably doing functional imaging, and a cross
> > application functional imaging file format is being created. The
> > University of Iowa contributers hope to have an implementation of the
> > NIfTY file format early this fall http://nifti.nimh.nih.gov/.  
> > 
> > Good Luck,
> > Hans J. Johnson
> > hans-johnson at uiowa.edu
> > 
> > 
> >  
> > 
> > On Thu, 2004-06-17 at 17:19, Jill Goldschneider 327 wrote:
> > 
> >>Hi,
> >>
> >>I have been having some problems writing Analyze (SPM extension I
> >>believe) formatted images where origin information is stored in
> >>the data_history's char originator[10] field.  (I believe this
> >>field was originally intended to hold a character string.)
> >>If I use the ImageReadWrite example with Dimension = 3, e.g.
> >>  ImageReadWrite image.hdr tmp.hdr
> >>tmp.hdr loses all of the information in the originator field,
> >>(and other fields as well).
> >>
> >>What I've found, is that on a sun solaris8 system, strncpy is
> >>actually NOT copying all 10 requested characters:
> >>
> >>    // try using [ 0 128 0 128 0 64 0 0 0 0 ] in tmp.c_str()
> >>
> >>    strncpy(this->m_hdr.hist.originator,temp.c_str(),10);//Note this is necessary because the array is not necessarily null terminated.
> >>
> >>    // look at contents of m_hdr.hist and temp.c_str,
> >>    // m_hdr.hist.originator is all 0!
> >>
> >>If I change this statement, and all other strncpy statements
> >>in the itkAnalyzeImageIO.cxx file, to use memcpy
> >>
> >>    memcpy(this->m_hdr.hist.originator,temp.c_str(),10);//Note this is necessary because the array is not necessarily null terminated.
> >>
> >>then everything works much better.
> >>
> >>Would someone please consider making this change?
> >>
> >>Thanks,
> >>
> >>Jill
> >>
> >>_______________________________________________
> >>Insight-users mailing list
> >>Insight-users at itk.org
> >>http://www.itk.org/mailman/listinfo/insight-users
> >>
> > 
> > 
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> > 
> 
> 
>