The fslroi tool extracts a continuous range of time points. The help
Usage: fslroi <input> <output> <tmin> <tsize>
For your situation you will need to extract each volume separately then merge them back together again.
fslroi AP_Scan 00.AP_Scan_b0 0 1
fslroi AP_Scan 15.AP_Scan_b0 15 1
fslroi AP_Scan 29.AP_Scan_b0 29 1
fslroi AP_Scan 43.AP_Scan_b0 43 1
fslmerge -t AP_Scan_b0 00.AP_Scan_b0 15.AP_Scan_b0 29.AP_Scan_b0 43.AP_Scan_b0
You can then use the AP_Scan_b0 image for your TOPUP. You will need to repeat the procedure for the PA scans and then merge the two scans together for your topup analysis.
fslmerge -t Scan_b0 AP_Scan_b0 PA_Scan_PA
You can certainly combine these steps but I was trying to as explicit as possible.
The TOPUP FAQ gives some information about the direction. http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP/Faq
As long as you are consistent the direction (-1 or 1) is not really relevant if you are only interested in correcting the distortion. If you want the fieldmaps to accurately measure the field inhomogeneity then you need to pay closer attention.
I hope this helps.
Bob
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