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. <[email protected]> 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. <[email protected]> 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
>>
>
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