Graham,
Thanks for pointing these out. We've corrected the page (but it still
needs quite a bit more work to make it a true 'file spec').
Nick
On Wed, 2006-07-12 at 20:05 -0700, Graham Wideman wrote:
> Folks: (Probably Nick S?)
>
> Comments on the MghFormat wiki doc page:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fMghFormat
>
> 1. Width/Height/Depth confusion.
>
> Doc says...
>
> width integer first dimension of the image buffer (slowest)
> height integersecond dimension of the image buffer (2nd slowest)
> depth integer fastest dimension when reading the buffer
>
> ... yet mriio mghWrite(...) source code says...
>
> for (frame = start_frame ; frame <= end_frame ; frame++) {
>for (z = 0 ; z < depth ; z++) {
> for (y = 0 ; y < height ; y++) { [...]
>for (x = 0 ; x < width ; x++)
>
> Ie: width should be fastest, and depth slowest, contrary to doc.
>
> Further, the statement "the bytes being read in the order Z --> Y --> X" is
> either incorrect or doesn't have any meaning.
>
> 2. "image data starts at specified offset, which is currently ???".
>
>
> Looks like from the source code that the header is padded to 24 + 256,
> which means image starting at byte 280 (counting from zero).
>
> 3. Other Data
> --
> In the doc, the Other Data section ends at "FoV". Actually the source code
> shows that mghWrite writes out other stuff beyond that, which in the
> examples I looked at appears to be a history of commands performed on the
> image so far, for example (abbreviated [...] and wrapped by me):
>
> ===
> [...]
> mri_convert /data/[...]/39174a/mri/rawavg.mgz [output filepath] --conform
> ProgramVersion: $Name: stable3
> $ TimeStamp: 06/06/07-04:10:32-GMT CVS:
> $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp
> $ User: graham Machine: gwlin[...]
> CompilerName: GCC Compile[...]
>
> mri_ca_normalize -mask brainmask.mgz nu.mgz [...] norm.mgz
> ProgramVersion: $Name: stable3
> $ TimeStamp: 06/06/11-05:41:45-GMT CVS:
> $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp
> $ User: graham Machine: gwlin[...]
> GCC CompilerVersion:
> [...]
> ===
>
> (Plus the source code suggests that if a Talairach transform has been
> applied it appears here in some form).
>
> -
>
> Graham
>
>
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