I have completed the preFS, FS, and postFS phases (without errors). So here is my problem:
When executing fmriVol, specifically line 286 of TopupPreprocessingAll.sh, an error occurred when executing fsl/bin/topup:
Topup::topup_clp::topup_clp: Unrealistic read-out time, should be in range 0.01-0.2 s
I carefully checked the read-out time calculation (line 222-266 of TopupPreprocessingAll.sh): Total_readout=EffectiveEchoSpacing*(ReconMatrixPE-1)
However, the value of EffectiveEchoSpacing in the actual script comes from line 266 of hcp_main_milgram_tcp_2023.sh, where DwellTime_fMRI="0.0000021". Therefore, the calculated read-out time is only 0.0002163. Perhaps we should use the "EffectiveEchoSpacing": 0.000580009" entry in the fmap JSON file instead. In that case, the calculated read-out time would be 0.05974, which is in the range 0.01-0.2 s.
Has anyone else encountered a similar problem, or does anyone have other solutions? Looking forward to your replies.
I have completed the preFS, FS, and postFS phases (without errors). So here is my problem:
When executing fmriVol, specifically
line 286ofTopupPreprocessingAll.sh, an error occurred when executingfsl/bin/topup:I carefully checked the read-out time calculation (
line 222-266ofTopupPreprocessingAll.sh):Total_readout=EffectiveEchoSpacing*(ReconMatrixPE-1)However, the value of
EffectiveEchoSpacingin the actual script comes fromline 266ofhcp_main_milgram_tcp_2023.sh, whereDwellTime_fMRI="0.0000021". Therefore, the calculated read-out time is only0.0002163. Perhaps we should use the"EffectiveEchoSpacing": 0.000580009"entry in the fmap JSON file instead. In that case, the calculated read-out time would be0.05974, which is in the range 0.01-0.2 s.Has anyone else encountered a similar problem, or does anyone have other solutions? Looking forward to your replies.