Dear Paul,
I think the config file is probably ok as it is. Your problem is that you will need an EPI template in the space of the FSL T1 template. I think the easiest for you would be to download the SPM EPI template and use that.
Note though that there is a good reason why we recommend using a T1 structural for the inter-subject registration. Some EPI sequences have very little useful tissue-type contrast and in those cases the best you can hope for is a rough registration of the brain outline.
Jesper
On 21 Nov 2013, at 15:51, Paul Chou <[log in to unmask]>
wrote:
> Dear all FSL experts
>
> I have an old fMRI dataset which didn't have any T1 structure image. I want to perform group analysis for this dataset and I think I need to modify the configure file for FNIRT (because the configure file which described in website is for high resolution T1 image based spatial normalization). The example of the FNIRT website only describe how to perform spatial registration for fMRI dataset via high resolution T1 image. My question is if I only have fMRI dataset and want to perform spatial normalization for this dataset (normalize to MNI_EPI template), which part of the configure file should be modified ?
>
> Thank you
>
> Best
>
> Paul
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