Hi Anna,
I think that it is probably a mistake in the tutorial instructions - the example_func2highres.mat file maps the functional data to the subject’s structural scan instead of to the MNI template. As you suggested, the example_func2standard.mat file is the one you need.
If you used nonlinear registration when running melodic, you will probably want to specify “-w example_func2standard.nii.gz” instead of “--premat=…”.
Hope that helps,
Eelke
> On 2 Feb 2016, at 15:30, Anna Pajkert <[log in to unmask]> wrote:
>
> Dear FSL-Experts,
>
> I have a problem with creating an input for the group ICA. In my analysis I preprocessed the resting state data with feat and then applied aroma. As next step you are recommending a registration to the standard space (http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/melodic/) using:
>
> applywarp -r ${j}/reg/standard.nii.gz -i ${j}/filtered_func_data.nii.gz -o ${j}/filtered_func_data_standard --premat=${j}/reg/example_func2highres.mat
>
> After applying this transformation for my aroma output (denoised_func_data_nonaggr) the functional images were displaced and a part of frontal lobe was missing in every data set. However, the problem disappeared after applying the example_func2standard.mat transformation. Do you know why the example_func2highres.mat transformation is not working for the aroma output?
>
> Thank you in advance for your help.
>
> Kind regards,
> Anna Pajkert
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