Dear Annelene,
>
> I'm trying to use applytopup to apply the distortion correction to a full fMRI run (600 repetitions), however, from what I can see the applytopup only takes the first volume (which I used to calculate the distortions), so I only get out 1 corrected volume. There is nowhere in the options of applytopup to input a full data set with 600 repetitions.
>
> If I try to substitute the first volume with the full dataset I get the following error message: ApplyTopup:: msg=Mismatched input files
> which presumably is complaining that there is now 600 repetitions in the forward directions, while only one in the reverse direction.
lets assume that your 600 file is called sixhundred, and also that a volume from the sixhundred was used as the first volume in your topup 4D input, then
applytopup --imain=sixhundred --inindex=1 --topup=my_topup --method=jac --interp=spline --out=my_output
should work.
The difference here is that by specifying --method=jac, instead of lsr which is default, you no longer have to have matched blip-up-blip-down volumes.
Jesper
>
> How do I get around this?
>
> Thanks!
>
> Annelene
>
> ########################################################################
>
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|