[MINC-development] micopy_all_var_values dies if non-standard variables are present in MINC files

[Peter NEELIN]

Hi Rick,

On Fri, 23 Jan 2004, Rick Hoge wrote:

> For a while we've been motivated to add 'custom' variables to MINC
> files to embed information about the experiment or analysis in a
> convenient way.  It seems though that non-standard variables prevent
> some of the MINC tools from running.

They shouldn't. That is one of the ideas behind minc. It should be
extensible, and as long as you don't use any standard variable names, you
should be okay. (One caution - I don't know if variables that are indexed
by image dimensions are always handled properly by programs that change
the dimensions, like mincresample.)

Anyway, I tried resampling the file fileWithNewVariable.mnc and it worked
fine on the SGIs in the BIC. Do you have an older version of mincresample?
Can you trace the problem down? The fact that it dies without an error
makes it hard to diagnose - the MINC package entry point just tells you
that a NetCDF function failed when called by the minc function
micopy_all_var_values, but NetCDF obviously did not report the error as it
should have. Are you certain that you have not simply run out of disk
space (or quota)? NetCDF does have a habit of swallowing that sort of
error.

You could try compiling a debugging version of mincresample and trace it
to find out where the problem occurs.

Are you using NetCDF 3.5? I think that it does a better job of reporting
errors than 3.2.

The only comment that I would have about your file is that you do not need
to have the dimension variables (xspace, etc) indexed by anything if the
spacing is regular. If you are not going to fill in the information, then
you should not have the indexing. Right now, the information is
contradictory and so your file is strictly speaking not valid.

For the imagemin/max variables, you do not need to have them indexed by
zspace if you are going to scale all of the images the same way.

            Peter
----
            Peter Neelin (neelin@bic.mni.mcgill.ca)