Hi Mark,

Thanks for the suggestion. I am trying to use pointflirt. Here are  
some questions I encountered.

1. After using the pointflirt as:  pointflirt -i input.txt -r ref.txt - 
o test.mat

I tested the result by using:  img2imgcoord  -src input.nii -dest  
ref.nii -xfm test.mat

( input.txt has 4 coordinates in voxels from input.nii. ref.txt has  
the corresponding points from ref.nii )

I found that I could not get a perfect match between the input and ref  
points, even if I confined the input and ref points on a 2-D surface.

2. The unit in input.txt should be mm or coordinate in voxels? How and  
why should I use --vox option in pointflirt?

Thanks.

Yunjie


On Oct 25, 2008, at 4:09 AM, Mark Jenkinson wrote:

> Hi,
>
> I'm afraid I am still not sure what you want.
>
> The "surface of the brain" is a convoluted shape in 3D
> and mapping a 2D image "onto" this would require
> something like flattening the cortical surface, which
> you could do with FreeSurfer.  If you are not wanting
> it to map onto the external cortical surface, but instead
> have a single 2D cross-sectional image of the brain
> and wish to find the right plane in 3D to map this to then
> you can either you flirt or pointflirt (which takes manually
> selected coordinates) to do this.
>
> I hope this helps.
>
> All the best,
> 	Mark
>
>
> On 24 Oct 2008, at 14:09, Yunjie Tong wrote:
>
>> Hi Mark,
>>
>> Thanks for the reply. I would like to register my 2-D image onto  
>> the surface of the brain by knowing several corresponding locations  
>> on the surface of the brain. In Matlab, I found a function cpselect  
>> which can register 2-D image onto another 2-D image using the  
>> projective mode. I am just wondering if flirt can do 2-D to 3-D  
>> registration using spatial markers instead of anatomical features.  
>> Thanks.
>>
>> Best,
>>
>> Yunjie
>>
>>
>> On Oct 23, 2008, at 6:16 PM, Mark Jenkinson wrote:
>>
>>> Hi,
>>>
>>> I'm not sure by what you mean when you say "wrap my 2-D image" or  
>>> "project
>>> a rectangular 2-D images ... onto the surface of a 3-D MRI brain  
>>> image".
>>>
>>> If the 2-D image corresponds to a cross section *through* the  
>>> volume of
>>> the 3-D image then this is fine.  If, instead, it consists of  
>>> values corresponding
>>> to "surface" voxels of the brain then it is not possible.
>>>
>>> It should be possible with flirt to register your 2-D slice onto a  
>>> 3-D image
>>> if you are in the first situation above.  In this case all you  
>>> need to do is use
>>> the 3-D image as the reference and the 2-D slice as the input,  
>>> although
>>> getting an initial orientation which is "close" is often critical  
>>> in these situations.
>>> You can either use pointflirt or nudge to help you with this.
>>>
>>> If this doesn't answer your question then please provide us with a  
>>> more detailed
>>> description of your problem.
>>>
>>> All the best,
>>> 	Mark
>>>
>>>
>>> On 23 Oct 2008, at 18:51, Yunjie Tong wrote:
>>>
>>>> Hi,
>>>>
>>>> I am trying to project a rectangular 2-D image (obtained from  
>>>> other imaging modality) onto the surface of a 3-D MRI brain  
>>>> image. I know the corresponding locations of the four corners (of  
>>>> my 2-D image) on the head. Can I use flirt to wrap my 2-D image  
>>>> on the head's surface based on those 4 locations (corners) ?  
>>>> Thanks in advance.
>>>>
>>>> Best,
>>>>
>>>> Yunjie
>>