[MINC-users] mincaverage error

[Lisa F. Akiyama]

Andrew,

I tried running the filelists with several different file orders, but
unfortunately the same error kept on occurring.


Claude,
I set the shell environment as you instructed, and ran a bunch of
minaverages on different subsets of all the files I have.
I have two sets of data - one from site S (28 files) and another from site I
(15 files) (a total of 43 files).

When I mincaveraged site S files one by one (2, 3, 4, 5...), no errors came
up and output files were created just fine.
When I mincaveraged site I files one by one (2, 3, 4, 5...), also no errors
came up and output files were created correctly.
When I mincaverated all site S files (28) and one file from site I (one of
the 15 files; tested all 15) (a total of 29 files being averaged), the error
came up for all trials and the output files were black images when displayed
in register.
When I took a few files from both site S and site I so that the total number
of files was 29, mincaverage gave me that error (I have not tested this for
all possible pairings).
But when I mincaveraged a few files from site S and a few from site I (I
have not tested this for all possible pairings - total number of files used
was not 29 in all trials), it seems like the output files are created fine
without any errors.

As far as I can tell, it seems like the site S and site I files have slight
differences in their headers.
When I view their headers using MIPAV, all seem to be the same except for
the 'Begin' values in the variable information section (below is an example
from a site I file):

Variable information:
> Name: rootvariable VSize: 4 Type: NC_INT  *Begin: 4512*
>   Attributes:
> Name: varid Value: MINC standard variable
>  Name: vartype Value: group________
> Name: version Value: MINC Version    1.0
> Name: parent Value:
>  Name: children Value: image
> processing
>   Variable value: -2147483647
> Name: xspace VSize: 4 Type: NC_INT  *Begin: 4516*
>   Attributes:
> Name: varid Value: MINC standard variable
> Name: vartype Value: dimension____
>  Name: version Value: MINC Version    1.0
> Name: comments Value: X increases from patient left to right
>  Name: spacing Value: regular__
> Name: alignment Value: centre
> Name: step Value: 1.0
>  Name: start Value: -96.0
> Name: direction_cosines Value: 1.0 0.0 0.0
> Name: units Value: mm
>  Name: spacetype Value: native____
>   Variable value: 0
> Name: yspace VSize: 4 Type: NC_INT  *Begin: 4520*
>   Attributes:
> Name: varid Value: MINC standard variable
> Name: vartype Value: dimension____
>  Name: version Value: MINC Version    1.0
> Name: comments Value: Y increases from patient posterior to anterior
>  Name: spacing Value: regular__
> Name: alignment Value: centre
> Name: step Value: 1.0
>  Name: start Value: -134.0
> Name: direction_cosines Value: 0.0 1.0 0.0
> Name: units Value: mm
>  Name: spacetype Value: native____
>   Variable value: 0


I'm not sure if all I've written above makes any sense at all or if it even
helps in trying to debug this odd error that I am seeing.
Please let me know if I should test all possible pairings for all of the
functions that I've carried out if that helps.

Thank you.


Best,
Lisa


On Sat, Mar 5, 2011 at 8:37 AM, Claude LEPAGE <claude at bic.mni.mcgill.ca>wrote:

> Andrew,
>
> > I think this bug might be related to one I have seen as of late (only
> > on Ubuntu Maverick and the latest Debian release). In combination with
> > various phases of the moon you get this self same error. Even
> > something as simple as changing the input files order can make it go
> > away. I have noticed it more with register than anything else but
> > still haven't seen anything all that consistent yet to track it down.
> > :(
>
> That's the Coriolis force effect. Why don't you try to run your
> job on a computer in the northern hemisphere?
>
> Lisa: if you can systematically reproduce your bug, then that would
> be a starting point for us to debug the code. Have you tested mincaverage
> on a different number of input files, like 2,3,4,..? Just for fun, set
> the shell environment variable VOLUME_CACHE_THRESHOLD=-1. Caching should
> have been disabled in minc 2.1.00, but just in case.
>
>
> Claude
> _______________________________________________
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>