I've not used FIRST, so I'm not familiar with your specific problem. Why would
you want to transform a subject-specific structure generated with FIRST into
standard space? If it is just to verify that each structure was identified
correctly, then you shouldn't need to worry about little things like
interpolation artifact. At any rate, this may be helpful:
http://www.fmrib.ox.ac.uk/fslfaq/#flirt_mask
Also, if you are worried about too much interpolation, you can use "-interp
nearestneighbor" with flirt.
On Sunday, November 13, 2011 18:04:51 you wrote:
> Hi, experts. I have a problem of how to transforma a volume into the
> standard space. After running run_first_all, I got a 4*4 matrix and a
> .nii.gz file containing the resulting substructures. But the substructures
> are in their native space. Now could I use the command flirt with the
> option applyxfm? But after this command, I fould the resultant voxel values
> are interpolated. As a result, each substructure is kinda like inflated.
> For example, arround the left hippo, there are a lot of values other than
> 17. Now my problem is, if I want to extract the left hippo, what should be
> the thresold value in order to keep its shape? Thanks a lot.
>
> Best,
> Jie
|