Hi,
That's almost right.
If you have not run any non-linear registration then
standard2example_func.mat is all that you need to
map from standard space to the functional space.
However, your reference image in the FLIRT call
should use example_func, not the T1 structural image.
So just run the command in Q2 using example_func
as the reference and it should be fine.
If you've used non-linear registration then you
need to do things differently.
All the best,
Mark
On 17 Jun 2010, at 19:49, Sang Lee wrote:
> Hello FSL,
>
> I am trying make a native space ROI mask using
> "standard2example_func.mat" matrix (that was created from Feat) and
> ROI mask that is in standard space (MNI152_T1_2mm_brain).
>
> Q1: Can we use this matrix (standard2example_fun.mat in .feat/reg
> directory) to do this?
> Q2: Is this the correct commandline to do this?
> flirt -applyxfm -init .feat/reg/standard2example_func.mat -in
> ROI_standardspace_maks -ref native_space_T1_struc_bet_brain -out
> native_space_ROI_mask
>
> When commandline in Q2 is complete, native_space_ROI_mask, is not
> projected properly (when checked with fslview, it appears to be
> shifted lower in y axis). We are worried that Feat might be adding
> additional parameters to make the standard2example_func.mat file.
>
> If Q2 commandline is completely wrong, could you suggest away to do
> this?
>
> Thank you for all your help in advance.
>
> From Sang
>
>
>
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