(QSIprep)Eddy Error AcqPara: Unrealistic read-out time(ds002330)

Hello all,

I am having an issue of preprocessing DWI data of ds002330(only sub-01) (Neuroimaging predictors of creativity in healthy adults) with QSIprep.

Before preprocessing, I copied “acq-lr_dwi.json” and “acq-rl_dwi.json” in BIDS root folder to sub-01/dwi folder.

HOWEVER, I have an issue in Eddy processing, which claim that EPI total readout time of your data is not “realistic” .

So, I can’t perform preprocessing this data.(can preprocess other data with QSIprep)

RuntimeError: Command:
eddy_openmp --cnr_maps --field=/scratch/qsiprep_wf/single_subject_01_wf/dwi_preproc_wf/hmc_sdc_wf/topup/fieldmap_HZ --field_mat=/scratch/qsiprep_wf/single_subject_01_wf/dwi_preproc_wf/hmc_sdc_wf/topup_to_eddy_reg/topup_reg_image_flirt.mat --flm=linear --ff=10.0 --acqp=/scratch/qsiprep_wf/single_subject_01_wf/dwi_preproc_wf/hmc_sdc_wf/gather_inputs/eddy_acqp.txt --bvals=/scratch/qsiprep_wf/single_subject_01_wf/dwi_preproc_wf/pre_hmc_wf/rpe_concat/merge__merged.bval --bvecs=/scratch/qsiprep_wf/single_subject_01_wf/dwi_preproc_wf/pre_hmc_wf/rpe_concat/merge__merged.bvec --imain=/scratch/qsiprep_wf/single_subject_01_wf/dwi_preproc_wf/pre_hmc_wf/rpe_concat/merge__merged.nii.gz --index=/scratch/qsiprep_wf/single_subject_01_wf/dwi_preproc_wf/hmc_sdc_wf/gather_inputs/eddy_index.txt --mask=/scratch/qsiprep_wf/single_subject_01_wf/dwi_preproc_wf/hmc_sdc_wf/pre_eddy_b0_ref_wf/enhance_and_mask_b0/topup_imain_corrected_avg_mask.nii.gz --interp=spline --data_is_shelled --resamp=jac --niter=5 --nvoxhp=1000 --out=/scratch/qsiprep_wf/single_subject_01_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected --repol --slm=linear
Standard output:
EDDY::: AcqPara::AcqPara: Unrealistic read-out time
EDDY::: EddyHelperClasses.cpp::: EDDY::AcqPara::AcqPara(const ColumnVector&, double): Exception thrown
EDDY::: Eddy failed with message EDDY::: ECScanClasses.cpp::: EDDY::ECScanManager::ECScanManager(const string&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, EDDY::ECModel, EDDY::ECModel, const std::vector&, const EDDY::PolationPara&, EDDY::MultiBandGroups, bool): Exception thrown
Standard error:
For your information, TotalReadoutTime in this data is 0.000910s

Thank you in advance.

Try .09779

It is calucated by 0.00077*(128-1)

seem a HCP style dwi recording.

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Thank you. I’ll try it.

I was able to perform preprocessing ds002330 when I changed TotalReadoutTime.

But, is it okay to change TotalReadoutTime of dataset?

You should definitely try to find out what the actual total readout time is. If you have access to the dicom data you should be able to get an accurate number from a recent version of dcm2niix


Thank you.

I used calculated TotalReadoutTime, referring to JSON file of dwi in dataset because I was not able to get DICOM.

FYI, I calculated TotalReadoutTime of other dataset, and it was corresponding to “TotalReadoutTime” written in JSON. However, in datasets I am using now, TotalReadoutTime calculated and written in JSON is not the same.

Calculated: 0.09779
JSON. : 0.000910

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