Re: Full analysis: prolate and oblate -- January 06, 2011 - 19:16

Ok, looks like "diff_min.py" is already setup to do everything I
wanted. :-) The problem with the prolate/oblate uncertainty still
exists though. I have a feeling that the constraint for Da=>0 or <=0
is removed by the statement fix('diff', fixed=False). As a workaround
at the moment I use the following in the "diff_min.py":

    fix('diff', fixed=False)
    cdp.diff_tensor.spheroid_type = 'prolate'

This seems to do the trick.

Vitaly




On Wed, Jan 5, 2011 at 16:14, V.V. <vvostri@xxxxxxxxx> wrote:
> Hello,
>
> I am trying to optimize the diffusion tensor outside of
> "full_analysis.py", to avoid this prolate/oblate issue. I understand
> that the first round should be models tm0-tm9, followed by model
> selection, while the latter ones should alternate between the tensor
> optimization and model-free parameters fitting. I am not entirely sure
> how to start though. Should I:
>
> 1. Take the results from 'local_tm/aic', fix spins, initialize the
> diffusion tensor and then run grid search + minimization, then fix the
> tensor and optimize model-free parameters?
>
> or
>
> 2. Fix spins, initialize the diffusion tensor and perform m0-m9 runs
> followed by model selection, and after that fix the tensor and
> optimize MF? This seems to be what "diff_min.py" does.
>
> Thank you,
> Vitaly
>
>
> On Sat, Dec 18, 2010 at 23:25, V.V. <vvostri@xxxxxxxxx> wrote:
> > Hello,
> >
> > I have performed a "full_analysis" run, and the Chi2 values for
> > prolate and oblate models were reported to be identical. I have
> > checked the contents of the /prolate/round_**/opt, and the results
> > file appears to contain the data for the oblate model:
> >
> > ================
> > <diff_tensor desc="Diffusion tensor" type="spheroid">
> > <Da ieee_754_byte_array="[144, 224, 168, 43, 17, 72, 82, 193]">
> >                -4792388.6821824461
> >            </Da>
> > <fixed>
> >                False
> >            </fixed>
> > <phi ieee_754_byte_array="[127, 197, 226, 164, 9, 205, 0, 64]">
> >                2.1001160508828316
> >            </phi>
> > <spheroid_type>
> >                'oblate'
> >            </spheroid_type>
> > <theta ieee_754_byte_array="[157, 42, 47, 69, 3, 109, 252, 63]">
> >                1.7766144468793421
> >            </theta>
> > <tm ieee_754_byte_array="[131, 104, 243, 90, 176, 172, 60, 62]">
> >                6.6763176508168525e-09
> > </tm>
> > </diff_tensor>
> > ================
> >
> > So, does it mean that the system is converging to the oblate model in
> > the prolate pipe? I thought the Da sign is constrained during the
> > search.
> >
> > Thank you,
> > Vitaly