Hi!
I used the BBR registration of functional to subject's MPRAGE and 12 DOF linear to MNI and the result. As viewed in FSL output looked correct.
For another type of analysis, I need to apply the transformations created in the above step to create functional images in the MNI space for each subject.
I did that by applying the following command:
/usr/local/fsl/bin/flirt -in smooth_func.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -out ${sub}smooth_func_2mmMNI152.nii.gz -init ${mypwd}${sub}/image/${datatype}/melodic_unwarp.ica/reg/example_func2standard.mat –applyxfm
The attached image shows that the resulting functional image is much inflated compared to the MNI standard brain (in red).
The above transformation was done on smoothed data. I repressed this on unsmoothed data, but the result did not change.
I need the functional brain to fit well to the standard for various reasons, such as using atlases or overlaying the image with tissue priors.
If you have any clue what may be wrong with what I am doing, this would be a great help!
Best,
Aga
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