Hello,
I'm having problems running the applytopup command.
We collected one DWI scan with 20 directions (b0 + 19*b=1000) as well as 2 smaller DWI scans with 3 b0 images of opposite phase encoding directions. I have run the following topup comand:
> topup --imain=15_16_17_PA_AP_AP --datain acqparams.txt --out=topup_params --iout=15_16_17_PA_AP_AP_corrected
with
> more acqparams.txt:
0 -1 0 1
0 -1 0 1
0 -1 0 1
0 1 0 1
0 1 0 1
0 1 0 1
0 1 0 1
and 15_16_17_PA_AP_AP.nii obtained using
> fslmerge -t 15_16_17_PA_AP_AP 15_PA 16_AP 17_AP
and 17_AP obtained using
> fslroi 17_AP 17-ep2d_advdiff_2mm 0 110 0 110 0 42 0 1
I then want to apply the calculated fields with applytopup, but I get an error:
> applytopup --imain=17-ep2d_advdiff_2mm --datain=acqparams.txt --inindex=7 --topup=topup_params --out=17-ap2d_advdiff_2mm_corrected
ApplyTopup:: msg=Invalid combination of phase-encode vectors for least-squares restoration
terminate called after throwing an instance of 'TOPUP::ApplyTopupException'
what(): ApplyTopup:: msg=Invalid combination of phase-encode vectors for least-squares restoration
Abort (core dumped)
The number of input arguments for --imain and --inindex (1) seems wrong, but i don't understand how I could have more than 1 input file since I only have one dataset to correct
Please help,
Julien
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