How to use 3dWarp for oblique correction?


I’m conducting preprocessing on resting state fMRI data and make alignment for anatomical and resting state fMRI data, with warning:

If you are performing spatial transformations on an oblique dset,
  such as ./101-BOLD-EC-volreg-lp-dt_temp+orig.BRIK,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running:
     3dWarp -deoblique
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.

I use 3dWarp -gridset 101-BOLD-EC-volreg-lp-dt_temp+orig -deoblique 101-BOLD-EC-volreg-lp-dt_temp+orig for oblique correction, with large part of the brain been cutted off, which makes me confused, are there any suggestions?


Do not provide a gridset, and 3dWarp will provide an adequate one.


Thanks for your immediate reply!
Is it possible for me to get the same grid as the original image? the default option of 3dWarp will output same voxel size in all three dimensions, while what i want is the original one (3.125 x 3.125 x 4.50) .
Moreover, it’s seems to have no effect to make adjustment for severely oblique image with both 3dWarp and some other warp commands, are there any good solution with these images?


I’m not sure why you need the grid to be the same as another dataset when clearly this is in a different space. Still, you can accomplish this in another step with 3dresample and specify the voxel dimensions. Furthermore, the output from this can be used as 3dWarp’s gridset option and the original 3dWarp command executed again with that difference and no additional interpolation.

Dear Glen,

I only have two subjects with oblique images, to reduce processing of the other subjects’ images, i want to remain the original grid of these two oblique images, is it reasonable?

I'm not sure why you need the grid to be the same as another dataset when clearly this is in a different space.

Besides, i am not quite clear for “this is in a different space” you said above, do you mean different grid?

What’s more, I have one extra image with large oblique angle, with little adjustment using 3dWarp and @auto_tlrc, could you give me some advice?