Hi Roberto,
I checked the logs and it appears that 4.1.5 is the first version
where it was properly present.
Jesper
> Hi Jesper,
> the --withaff is new, isn't it?
>
> thanks,
> roberto
>
> On Tue, Mar 23, 2010 at 1:46 PM, Jesper Andersson <[log in to unmask]
> > wrote:
>> Dear Giovanni,
>>
>>> suppose you computed the jacobian of a non linear transformation,
>>> to match
>>> the image A on the atlas B. I know the corpus-callosum mask in the
>>> atlas B.
>>> For computing the mean value of the jacobian in that mask, do I
>>> have to
>>> apply the non linear warping field to the jacobian before
>>> computing the
>>> mean?
>>>
>>> Ex.:
>>> fnirt --ref=atlas_B --in=A --config=config.cnf --cout=nonLinear
>>>
>>> fnirtfileutils --in=nonLinear --ref=atlas_B --jac=jacobian
>>> --out=nonLinear_warpField
>>>
>>> applywarp --ref=atlas_B --in=jacobian --warp=nonLinear_warpField --
>>> rel
>>> --out=jacobian_warped
>>>
>>> Do I have to use "jacobian" or "jacobian_warped" to compute the
>>> mean of
>>> jacobian in the corpus-callosum mask drawn in atlas_B?
>>
>> the Jacobian is calculated in the space of the --ref of the call to
>> fnirt.
>> So in your case you should be fine with using "jacobian".
>>
>> Note that you can get it directly from fnirt by specifying also the
>> --jout
>> parameter. Note also that the output of the --jout gives you the
>> Jacobian of
>> the non-linear mapping, as does fnirtfileutils when used as above.
>> If you
>> set also the --withaff flag in your call to fnirtfileutils you will
>> get the
>> Jacobian of the full transform (affine and non-linear).
>>
>> Good luck Jesper
>>
>
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