Hi, I have a subject for which it was acquired 4 images:
AP_1: 84 volumes
AP_2: 85 volumes
PA_1: 84 volumes
PA_2: 85 volumes
I ran topup with the following command:
topup --imain=Pos_Neg_b0 --datain=acqparams.txt --config=${topup_config_file} --out=topup_Pos_Neg_b0 -v
Where Pos_Neg_b0 has 4 volumes: the b0 of PA_1, then b0 of PA_2, b0 of AP_1, b0 of AP_2
Then I applied the topup to get the nodif_brain_mask from the hifib0
Finally, I ran eddy_cuda with the following command:
eddy_cuda --imain=$imain --mask=$mask --index=$index --acqp=$acqp --bvecs=$bvecs --bvals=$bvals --topup=$topup --out=$out --fwhm=10,0,0,0,0 --repol --resamp=lsr --fep --ol_nstd=5 --ol_type=both --slspec=$specFile --mporder=4 --very_verbose --s2v_niter=10 --cnr_maps
where $imain=Pos_Neg which has 338 volumes
index.txt has 84 columns lines with the number 1, followed by 85 with number 2, 84 with number 3, 85 with number 4. I am sure acquisition parameters file is correct ($acqp). bvecs and bvals have correct number of columns (338).
The command run with no problems at all, no warnings and no errors. And the output looks very good... but it has half volumes!! 169 volumes. So, I cannot run dtifit because it has different number of volumes than rotated_bvecs columns that is still 338.
What am I doing wrong?
Thanks!!
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