Dear Chao-Gan,
That file does have the information about an affine mapping between MNI
space and the template, but there are not many functions within SPM8 that
can make use of it. Only the normalise to MNI space function can currently
read it.
Best regards,
-John
2012/1/9 YAN Chao-Gan <[log in to unmask]>
> Thanks, John!
>
> OK, then I will segment single_subj_T1 and use these information to align
> the images in MNI space to the DARTEL template.
>
> Sorry, I made a type error, I wonder if "Template_6_2mni.mat" generated by
> DARTEL have the information from MNI space to the DARTEL template?
>
> Thanks!
>
> Chao-Gan
>
>
> 2012/1/9 John Ashburner <[log in to unmask]>
>
>> The spm8/canonical/single_subj_T1.nii image is only approximately aligned
>> to MNI space via an affine transform. If I remember correctly, this
>> subject is the same one that was labelled for the AAL atlas.
>>
>> The Sub001_seg8.mat is generated by the segmentation, and will give
>> approximate alignment of the subject to MNI space. See Klein et al
>> (NeuroImage) for an idea about the alignment accuracy compared with that of
>> Dartel.
>>
>>
>> Best regards,
>> -John
>>
>> 2012/1/4 YAN Chao-Gan <[log in to unmask]>
>>
>>> Thanks, John!
>>>
>>> Sorry the original message is not posted by me, I was thinking about a
>>> related question.
>>>
>>> I am not sure if I understand correctly: Is
>>> "spm8/canonical/single_subj_T1.nii" in MNI space and can represent every
>>> image in MNI space (such as AAL template, BA template, brainmask.nii,
>>> etc.). We segment this single_subj_T1 and use these information to align
>>> the images in MNI space to the group DARTEL template (get the flow field).
>>> I wonder if this step can be replace by using *Sub001_seg8.mat which is
>>> generated by DARTEL normalize to MNI space?
>>>
>>> Thanks!
>>>
>>>
>>> Chao-Gan
>>>
>>>
>>>
>>>
>>>
>>> 2012/1/4 John Ashburner <[log in to unmask]>
>>>
>>>> Sorry, but I misunderstood your original question. When you said
>>>> transformation matrix, I assumed that you meant affine transformation
>>>> matrix. The deformation fields for nonlinear registration are not really
>>>> matrices (although you can conceptualise the combination of spatial
>>>> transformation and interpolation as being the result of multiplying by a
>>>> very large sparse matrix).
>>>>
>>>> The AAL atlas is just based on the brain of a single subject, which has
>>>> been affine transformed to MNI space. Therefore, you'll need to find the
>>>> deformation that warps this subject so he matches your Dartel template. To
>>>> do this, you could try running the segmentation on a copy of the
>>>> spm8/canonical/single_subj_T1.nii file to generate imported GM maps, and
>>>> then running the "Run DARTEL (existing templates)" option to bring this
>>>> into alignment with your Dartel template data.
>>>>
>>>> When you have used Dartel, you can warp the AAL atlas to match your
>>>> subject as described in section 42.4 of the SPM8 manual (Warping one
>>>> individual to match another). As you are warping an image of labels, you
>>>> should change the interpolation to nearest neighbour.
>>>>
>>>> Best regards,
>>>> -John
>>>>
>>>>
>>>>
>>>>
>>>> 2012/1/4 YAN Chao-Gan <[log in to unmask]>
>>>>
>>>>> Dear John,
>>>>>
>>>>> Then M ("M is the appropriate matrix") is very important to get. In
>>>>> Unified Segmentation, we can get it from **_seg_inv*.*mat* . For the
>>>>> instance in New Segment + DARTEL, how can we get it?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Chao-Gan
>>>>>
>>>>>
>>>>> 2012/1/4 John Ashburner <[log in to unmask]>
>>>>>
>>>>>> It's not so straightforward to do this sort of thing by clicking
>>>>>> buttons via the user interface, but if you know how to code in MATLAB there
>>>>>> are some functions in SPM that could help. Essentially, you could do
>>>>>> something similar to the following...
>>>>>>
>>>>>> P=spm_select(2,nifti,'Select DTI and AAL');
>>>>>> V=spm_vol(P);
>>>>>> V(2).mat = M*V(2).mat; % where M is the appropriate matrix.
>>>>>> spm_reslice(V,struct('mask',false,'mean',false,'interp',0,'which',1,'wrap',[0
>>>>>> 0 0],'prefix','r'));
>>>>>>
>>>>>> Best regards,
>>>>>> -John
>>>>>>
>>>>>> 2012/1/1 ÀîÎÀÄÈ <[log in to unmask]>
>>>>>>
>>>>>>> Dear friends,
>>>>>>>
>>>>>>> I have the transformation matrix from MNI space to DTI space, is
>>>>>>> there anyway that I can transform the AAL template to DTI space by spm8?
>>>>>>>
>>>>>>> Thank you and happy new year.
>>>>>>>
>>>>>>>
>>>>>>> Weina
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
