[MINC-users] failures when running N3withsmallsmoothingdistances

[Andrew Janke]

Hi again Vitali,

I took a bit of a look at this the other day and yes found that there
is something strange going on with smaller step sizes.  Unbeknown to
me Claude also was looking at N3 and not only found this bug too but
fixed it.

We are currently testing this fix to N3 as it will mean a change in
how N3 behaves in some other cases. We will let the list know as soon
as this new release is ready for "public consumption".

For now I would suggest that you scale your data (either using a .xfm
or just mincedit) to make the data "about head sized" and give that a
go. (1mm steps, about 250mm across the volume, 50-150mm distance
parameter).

Thanks


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883


2009/5/5 Vitali Zagorodnov <ZVitali at ntu.edu.sg>:
> I managed to install the latest versions. Both problems are still there.
>
>
> In case of problem #2, there is an extra line in the error message:
>
> /usr/local/bic/bin/nu_correct -clobber -distance 10 001.mnc N3m.mnc
> -iterations 1000 -stop 0.000100
> Processing:.............................................................
> Done
> terminate called after throwing an instance of 'std::bad_alloc'
>  what():  std::bad_alloc
> nu_estimate_np_and_em: crashed while running spline_smooth (termination
> status=6)
> nu_correct: crashed while running nu_estimate_np_and_em (termination
> status=65280)
>
>
>
> -----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, May 05, 2009 12:29 AM
> To: MINC users mailing list
> Subject: Re: [MINC-users] failures when running
> N3withsmallsmoothingdistances
>
> 2009/5/5 Vitali Zagorodnov <ZVitali at ntu.edu.sg>:
>> Errr.. My Linux skills are quite rusty. How do I force installation to
>> use older gcc compiler?
>
> The simplest is to just do this before you run configure..
>
>   $ export CC=gcc-4.1
>   $ export CXX=g++-4.1
>
>> Yes, I am installing from source. For built packages, I don't know how
>> to change default installation directory, which should be
>> /usr/local/freesurfer/mni
>
>   $ ./configure --prefix=/usr/local/freesurfer/mni
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
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