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

[Rick Hoge]

Thanks for the quick reply!  I put an example at the following URL:

http://www.nmr.mgh.harvard.edu/~rhoge/stuff/fileWithNewVariable.mnc

Perhaps I have screwed the file up in some way, but the single 
modification of writing the file without any new variable seems to fix 
my problems with micopy_all_vars.

Actually, any comments on the validity of this file would be welcome - 
building MINC files from scratch (as this was done) has seemed a bit 
tricky.  One thing you may notice in this sample is that the xspace, 
yspace, and zspace lists contain all zeros (what uses these lists?  I 
guess these are to support non-uniform slice sampling?).  Also I was 
lazy and wrote the same min and max values for all images:

Rick


P.S. Here's an excerpt of the end of the minc header - how should these 
lists be defined?


data:

  zspace = 0, 0, 0, 0, 0, 0, 0 ;

  yspace = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0,
     0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0,
     0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ;

  xspace = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0,
     0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0,
     0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ;

  rootvariable = 0 ;

  image-min = -5.20979118347168, -5.20979118347168, -5.20979118347168,
     -5.20979118347168, -5.20979118347168, -5.20979118347168, 
-5.20979118347168 ;

  image-max = 18.2953414916992, 18.2953414916992, 18.2953414916992,
     18.2953414916992, 18.2953414916992, 18.2953414916992, 
18.2953414916992 ;

  MyNewVariable = 0 ;


On Jan 23, 2004, at 12:58 PM, Robert VINCENT wrote:

> Rick,
>
> Yes, it should work, but it wouldn't surprise me if it didn't!
>
> Please send one (or more) of your files and I'll see if I can fix it.
>
> 	-bert
>
> On Fri, 23 Jan 2004, Rick Hoge wrote:
>
>>
>> Hi -
>>
>> 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.
>>
>> The following is an example:  the file tmap.mnc has a variable added
>> containing information about the analysis performed, and we are 
>> running
>> MINC Version 1.0
>>
>> mincresample -like norm30.mnc tmap.mnc junk2.mnc
>> micopy_all_var_values: MINC package entry point
>>
>> Note that we don't want to use the history variable because we want a
>> specific parameter that can be queried in subsequent analysis steps.  
>> I
>> was under the impression the MINC/NetCDF should be extensible in this
>> way without breaking tools that don't know about all the variables
>> present.
>>
>> How should this be handled - does the MINC standard prohibit new
>> variables?  Thanks for any advice.  I can put such a file on /scratch/
>> if anyone is interested.
>>
>> Rick
>>
>>
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