[MINC-users] nonlinear transformation

[D. Louis Collins]

Rezwan,

I just realized that you are using the average305 target for non-linear 
registration.  We have stopped using it because of problems similar to 
those you've shown (but ours have not been as big).

Please use one of the newer icbm targets available from 
packages.bic.mni.mcgill.ca.

  mni-models-icbm152-lin

is better, but you still might have some errors.  the best is a new 
symmetric non-linear average of the 152 icbm subjects.  We are working 
to get it placed on the web.  should be soon.

-Louis


On Nov 22, 2005, at 10:24 AM, Rezwan Ghassemi wrote:

> here is the linear registration.
>
>
> --- "D. Louis Collins" <louis.collins at mcgill.ca> wrote:
>
>> Rezwan,
>>
>> that is pretty funny - the result looks very square.
>>
>> Can you show a result of the linear registration?
>> I'd like to see the
>> same slices if possible.
>>
>> -L
>>
>> On Nov 22, 2005, at 9:34 AM, Rezwan Ghassemi wrote:
>>
>>> Hi,
>>>
>>> I have also tried it. the attached file is output
>> of non-linear
>>> transformation
>>> to stx 305 model.
>>>
>>> Would you please let me know what is wrong with
>> it?
>>>
>>> thanks
>>> Rezwan
>>> --- "D. Louis Collins" <louis.collins at mcgill.ca>
>> wrote:
>>>
>>>> Oliver,
>>>>
>>>> Please post a few screen shots of the problem and
>> I
>>>> should be able to
>>>> give you some pointers.
>>>>
>>>> -Louis
>>>>
>>>>
>>>> On Nov 21, 2005, at 8:30 AM, Oliver Winz wrote:
>>>>
>>>>> Hello everybody,
>>>>>
>>>>> i have a problem concering nonlinear
>>>> transformation to stereotaxic
>>>>> space. The final MRI after transformation is
>> very
>>>> suspect. Maybe i
>>>>> forgot a very important part in the processing
>>>> steps and someone can
>>>>> give a hint.
>>>>> Here is my complete procedure:
>>>>>
>>>>>
>>>>>> dcm2mnc input*.IMA destdir/
>>>>>> mritotal inputMRI.mnc outputTrans-Lin.xfm
>>>>>> mritotal -nonlinear -transformation
>>>> outputTrans-Lin.xfm inputMRI.mnc
>>>>> outputTrans-NonLin.xfm
>>>>>> mincresample -transformation
>>>> outputTrans-NonLin.xfm -like
>>>
>>>>> average305.mnc inputMRI.mnc outputMRI-toTAL.mnc
>>>>>
>>>>>> mritotal -version
>>>>> Program mritotal, built from:
>>>>> Package MNI AutoReg, version 0.98r, compiled by
>>>> owinz at medpc66
>>>>> (i686-pc-linux-gnu) on 2005-02-24 at 17:58:14
>>>>>
>>>>> I'm working on Pentium V 3.0 GHz, running SuSE
>>>> Linux 9.2 with kernel
>>>>> 2.6.8-24.18-smp
>>>>> I get the DICOM MRI's from a Magneton VISION 1.5
>>>> T, Siemens, Erlangen,
>>>>> Germany) using a 3D T1-weighted MPRAGE sequenze
>>>> (voxel size = 1 x 1 x
>>>>> 1 mm³)
>>>>>
>>>>> Everyone who's interested in a screenshot,
>> please
>>>> let me know, i will
>>>>> send to you.
>>>>> Thanks in advance!!
>>>>> Greetings,
>>>>> Oliver
>>>>>
>>>>>
>>>>>
>>>>> -- 
>>>>> Oliver Winz, M.Sc.
>>>>> Molecular Neuroimaging Group
>>>>> Institute of Medicine (IME)
>>>>> Research Centre Juelich
>>>>> D-52425 Juelich
>>>>> Germany
>>>>>
>>>>> Phone: +49 2461 61-6493
>>>>> Web: http://www.fz-juelich.de/ime/mni
>>>>> Location: Building 15.9, Room 3010
>>>>>
>>>>> _______________________________________________
>>>>> MINC-users at bic.mni.mcgill.ca
>>>>>
>>>>
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> MINC-users at bic.mni.mcgill.ca
>>>>
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>
>>> <non-linear.jpg>
>>
> <linear_to_stx.jpg>