[Gate-users] Interfile format for STIR

[kangh at mskcc.org]

Hello all,

I have posted a question to the STIR user list and someone suggested to
post it to the GATE user list.

I am trying to use STIR to reconstruct simulated data using GATE, and I
have a question about the input intefile format for STIR.

STIR seems to require its own interfile format as input.  The intefile
format seems to be different from the Intefile 3.3 standard.  When I
"manip_image" on a header file in the standard Interfile 3.3 format (I
think) generated with medcon, I have gotten the following warning for
each parameter
   WARNING: KeyParser warning: unrecognized keyword: 
At the end of the message I have gotten another message
  ERROR: DiscretisedDensity::read_from_file: m000-sel_CT_scan.h33 seems
n unsupported file format

I would to know how to convert the Interfile 3.3 standard header and
image files generated with medcon to the input format for the STIR
executables. I tried to look at the web site
http://www.HammersmithImanet.com/~kris but I got a "not found" message
on the web, I just found several email in the stir-user archive saying
that the web site does not.  

I am wondering whether there is any existing STIR executable converting
the interfile 3.3 standard to .hv or I have to convert myself.  If I
have to convert it what parameters I should specify.  I assume that the
website should tell us what to do.  I could not find more information in
the user's guide other than the following in section 4.7.1.2.  

Thanks,

Hyejoo

4.7.1.2 Interfile The most comprehensively supported file format in the
library
is a newly proposed version of interfile. More details about this type
can be found
on http://www.HammersmithImanet.com/kris. Interfile image files are
written
as a pair of files image filename.hv, image filename.v
where image filename.hv is the header text file and image filename.v is
the data file.
In addition, we currently write a .ahv file which uses Interfile 3.3
conventions, with
a tweak for the slice thickness keyword to work-around an AnalyzeTM bug
(see
the comments for write basic interfile image header() in
STIR/IO/interfile.cxx).
The .ahv file is probably also readable by other programs capable of
reading Interfile
3.3.
If this output file format is used, and a filename without extension is
specified for
output, or when the filename has an extension .hv, the above naming
conventions
hold. If a filename with another extension is specified, this name is
used for the
name of the binary file.
When a file must be specified for reading as a parameter for a STIR
utility or
reconstruction program, the name of the .hv header file should be given.
Warning The interfile 3.3 standard does not allow to specify scale
factors for
the data. Hence, the .ahv file has no scale factors. This means that any
program
that reads the .ahv file will have improperly scaled images, unless the
scale
factor is 1. However, when using float output, STIR automatically writes
data with
scale factor equal to 1, so as long as your non-STIR program knows about
float
data, everything will be all right. The newly proposed Interfile
standard does use a
scale factor, and the .hv file follows this convention. However,
currently probably
only STIR programs know about this convention.




 
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