[MINC-development] Re: [MINC-users] Re: [geeks] voxel loop

[Peter NEELIN]

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On Fri, 28 Nov 2003, Maxime Descoteaux wrote:

> My problem is that I run out of memory on full brain mr images.  I need
> help setting things up?  I normally have "Volume" data structures lying
> around (too many)!  Why?
>
> Well, I do a multiscale vessel extraction. So, at all time and for every
> scale, I need six volumes to compute the symmetric Hessian matrix of [...]
>
> So, I also have 5 other volumes to save the output of the analysis
> [...]
> This is a lot of volumes lying around....  Is voxel_loop a solution to my
> problem?  I am not quite familiar with the buffer idea and I am not quite
> sure on how to set things up...

No. Voxel_loop is not designed for neighbourhood operations. You could
probably kludge it to do that, but I don't think that that would be a good
idea.

You can use volume_io to create temporary volumes that are cached - that
essentially swap to disk. You have to either set an environment variable
to force caching or make a library call. You also have to play around a
bit to make sure that the temp files live where you have disk space (if
/tmp is not large enough).

I've just had a look - I have an old example that tries to do this. You
might want to play around with it. I've attached it.

Note that you can do caching in two modes: random access and slice access.
Random access caches blocks of data. Unfortunately, reading a single block
requires reading much more than the block since files are organized by
rows. Slice access caches rows and so it does not thrash so badly. Random
access will be better on memory in the general case, but really needs an
underlying data organization that has a similar block structure (not yet
supported in minc). So use slice access. You will probably be iterating
over rows anyway, so it should work for you.

Just for comparison, one test case that I ran took 55 seconds without
caching, 97 seconds with slice access and 430 seconds with random access.
This was with 85 MB of image data on a 64 MB machine, so obviously it was
faster to let the machine swap than do caching. (Hmmm... that's not very
encouraging!) Anyway, play with it and see how it goes - much depends on
how you access the data.

Have fun!

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



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