[MINC-users] mincmorph problem

[Daniel Schwarz]

Hi Andrew, 

Thanks for your advice. It fixed the problem.
I use the package made for Cygwin by Dylan D. Wagner (I am not sure which
version of minc tools is there).

Daniel

-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca
[mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Andrew Janke
Sent: Tuesday, November 29, 2005 3:36 AM
To: MINC users mailing list
Subject: Re: [MINC-users] mincmorph problem

Hi daniel,

I presume test-segmented.mnc is a somewhat large file?

volume_io has provision for on-disk caching when working on large files.
unfortunately it was never completely implemented (as you have
discovered) this is mainly as memory is now cheap.

Which version of minc are you running?  later version have this
"functionality" essentially disabled by setting the cache threshold rather
large.  You could test this by doing something like this in your ~/.bashrc

   export VOLUME_CACHE_THRESHOLD 1000000000


a

On 28/11/05, Daniel Schwarz <schwarz at cba.muni.cz> wrote:
> Dear minc-users,
>
> I have afollowing problem with running mincmorph. All I would like to 
> do is to prepare mask files for my native MRI data. I would like to 
> use these mask files in nu_correct.
>
> After the command:
>
>    mincmorph -dilation test-segmented.mnc test-dilated.mnc
>
> I get the message:
>
>    Not implemented yet in cache_volume_range_has_changed()
>    Not implemented yet in cache_volume_range_has_changed()
>    Copy_volume(): copying cached volumes not implemented.
>    Segmentation fault (core dumped)
>
> I tried two ways to construct test-segmented.mnc:
>
> mincmath  -segment -const2 100 4096 -byte -unsigned -range 0 1 
> test.mnc test-segmented.mnc mincmorph -binarise -range 100 4096 
> test.mnc test-segmented.mnc
>
> with the same result from dilation.
> I guess that the problem is is in the messages Copy_volume...., as the 
> messages Not implemented yet in.... are quite frequent.
>
>
> Can anyone give me a suggestion to solve that problem?
> Is there another way to do the mask files for nu_correct from native MRI?
> I could do also nu_correct in stx space, where the maskfiles are 
> prepared, but the image intensities are already blurred by 
> interpolation...and phpwiki also suggests to perform nu_correct on native
MRI.
>
> Thanks for any replay.
>
> Regards.
>
> Daniel Schwarz
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012

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