Dear Charlotte,
>
> I have a PA.nii image from my imaging session and I would like to use it for distortion correction. However, I have some trouble with the use of the topup command.
>
> 1) first I need to get a AP image, thus I use the fsl roi command:
>
> fslroi <rsfMRI.nii> nodiff 01
>
> Here I don't get an nodiff image.
I would need a bit more info here. What do mean when you say you don’t ge a nodiff image? Do you get an error message?
>
> 2) Then I need to merge the nodiff image and the PA image, as I need it for the topup command.
>
> fslmerge -t AP_PA <nodiff> <PA_rsfMRI>
>
> I have tried with using the rsfMRI.nii data as nodiff, but then I still don't get a merged image called AP_PA.
Same here. Do you get an error message?
Jesper
>
> Notice. I know that it is originally for diffusion imaging, however, I'm using this for my resting state data, as I have been told that I can do so.
>
> Best,
> Charlotte, Master student in Neuroscience and Neuroimaging
>
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