I am trying to run FSL EDDY on a multishell diffusion scheme (5 shells total of 142 directions plus 3b0). The data has been recorded in Siemen's prisma scanner. I am using fsl5.0.9 version. (2015 version)
After running topup when I am trying to run eddy_openmp I am encountering the following error
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I'm thrown
terminate called after throwing an instance of 'EDDY::KMatrixException'
what(): KMatrixException: msg=MultiShellKMatrix::SetDiffusionPar: Data not shelled
Aborted (core dumped)
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When I read the eddy manual it seems eddy tries to figure out that whether there is sufficient number of direction per shell to perform its operation properly however there supposed to be a flag --data_is_shelled which was supposed to force eddy to bypass this test however in fsl5.0.9 which is the newer version this option doesn’t seem to be activated. simplying giving the option
time eddy_openmp --imain=DWI_input.nii.gz --mask=corrected_b0_AP_PA_Tm_brain_mask.nii.gz --acqp=my_acq_param1.txt --index=index.txt --bvecs=DWI_rotbvec.bvec --bvals=DWI.bval --topup=my_topup_results --out=eddy_corrected_data1 --data_is_shelled
gives the message
--data_is_shelled: Option doesn't exist!
If someone could help me to circumvent this issue that will be really great. I have a urgent deadline to meet.
Thanking you
sourajit
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